Many secular Muslims seem to hate the U.S., Israel, and even Christians living among them, just as passionately as their religious brothers do, but in a form that is political rather than religious. In Islam, there is no separation of religion and state: Muslims might even be atheists, but they may bring to their atheism many of the values of the cultures around them.
The inability to abandon old views might be typical of all cultures: it is so much easier to retain habits – such as the disparagement of other races or gender -- and when circumstances change, to dress them up in different clothes. This seems particularly true regarding peoples' views of the "other," whatever the particular form might take of "different from me." We all often have difficulty abandoning old feelings towards those we do not like -- especially when those feelings become socially and politically acceptable, or even encouraged. When such inhibitions are removed, we often do not change our views, but merely the reasons for why we hold them.
In Russia, for example, the view of Jews both during the Tsarist Empire and under the Communists, as that the Jews were hated ostensibly because they had committed "deicide" -- killing the Christian Lord, Jesus. Later, under the Communists, when Jews did their best to disavow their religion and ethnic origin, and put Judaism behind them to assimilate and become the ultra-secular "New Soviet Man," the Russian Orthodox Christian Communists still hated Jews. But now, the Christians claimed, they did not hate the Jews for supposedly killing Christ; instead, they said they hated the Jews for being "cosmopolitan" -- implying that their allegiance was not wholeheartedly to the Soviet Union. The old Russian sentiment remained.
In the Muslim World
Before the Islamist takeover of Turkey in 2002, senior Turkish secular political and military leaders often blamed the U.S. for supporting Greece: Greece was Christian and Turkey, though secular, was Muslim. Because both Greece and the West were Christian, they claimed, Turkey was therefore fated to remain an outsider in the Western club. Some members of the Turkish secular elite apparently felt that being even a secular Muslim was such a barrier to Western acceptance that privately they excoriated Ataturk for not making the Turks abandon Islam and adopt Christianity. To compound their feelings of frustration at not being accepted as Westerners, they often brought up a story about the Turkish Sultan Mehmed the Conqueror, who seized Constantinople [Istanbul] from the Greek Christians in 1453. According to this story – which may or may not have been true -- after Constantinople had been subdued, Mehmed thought long and hard about whether to remain a Muslim, or to convert to Greek Orthodox Christianity. In the end, Mehmed chose to remain Muslim. Had he converted, these secular Turks lamented, modern Turkey would have been Christian and had no problem being embraced by the West.
Many Turks also have difficulty understanding that in the West, there could be political and religious animosity among some Christians against Jews. Deep within the Muslim culture, "all non-Muslims are one entity" allied against the Muslims. The classic Islamic view is that there are two worlds – the World of Islam (Dar al-Islam) and the World of War (Dar al-Harb) which will be forever locked into conflict, at least until all the non-Muslims submit to the peace of Islam. The Muslim view -- with the division between Sunnis and Shi'ites overlooked -- goes on to claim that all Muslims are one people.
So even though these secular Turks might feel deeply aliened from Islam -- they eat pork, drink alcohol, do not fast on Ramadan, and some explicitly say that they are not even Muslims -- their view of themselves can still be rooted in Islamic culture both toward themselves and toward others.
Some years ago, for instance, on a trip to the Iranian holy city of Ghom [Qom], a young Iranian mentioned that he was Communist, that he hated religion, and was only visiting Ghom to accompany his religious mother to pray at the shrine. When the conversation turned to the civil war in Lebanon, where many religious and ethnic groups were fighting each other, and we asked whom he supported, he replied that as a good Communist, of course he supported the poor Muslims who were by exploited by the rich Christians. When reminded that there were also rich Muslims exploiting poor Christians, he looked confused, and said, "But we have to support our Muslim brothers" -- the classic Islamic view that all Muslims are brothers against the non-Muslims, dressed in modern clothes. So much for "communism."
Christians and Muslims in the Galilee
Christians and Muslims live in close proximity in the Israeli Galilee. Islamic religious law defines Christians and Jews as fellow monotheists, "People of the Book." In Islamic culture, however, they are called "dhimmis," -- tolerated, second-class citizens who have the right to live under Muslim rule, but only as political and social inferiors who must pay for "protection" not to be looted or otherwise abused. Galilean Muslims often say Christians are pagans because "they believe in saints," i.e., they deify Jesus who was a human being, which is anathema in Islam. If Christians are supposed to be People of the Book, they cannot be pagans. Sunni culture -- like in the Galilee - often brands them as such.
Sunni Muslims often express similar reservations about their fellow Shi'ite Muslims who revere Imams, the descendents of their prophet Muhammad -- also apparently too close to polytheism for comfort.
In the extreme, this exclusionary view has culminated in the radical Sunni branch of Islam and the ruling philosophy of Saudi Arabia, Wahhabism, which brands Shi'ites as apostates, and whose followers do not even regard Shi'ites as fellow Muslims.
As the Saudis claim that people gather at the graves of Muhammad's family and his companions to "worship" the people buried there, the Wahhabis have systematically destroyed the graves and called the Shi'ites apostates. The Shi'ites reply that they although they have deep respect for their Imams and other great leaders, they do not deify their Imams.
Even though, therefore, according to Islam, all Muslims are brothers, when Islamic culture clashes with the rules of Islam, culture wins.
Iraq after Saddam Hussein
In Post-Saddam Iraq, besides Sunni-Shi'ite conflicts, both sides have increasingly made life so difficult for native Iraqi Christians that they have felt it necessary to flee Baghdad for areas in the north where Christians predominate, or else for Kurdish areas. The Kurds, mostly Sunni, seem to have more of the classical respect Islam requires towards non-Muslim dhimmis as fellow monotheists. The Kurds, therefore, seem more prepared to respect the classic rules of Islam than many of the Arabs whose ancestors brought Islam to the world.
The Egyptian "Arab Spring" and the Non-Muslims
Many of the leaders who started the revolt against Mubarak were predominately secular, but nonetheless seem to have retained their animosity not only toward Israel, but also toward the Egyptian Copts, the original population that inhabited Egypt for three and a half millennia before the Muslim onslaught in the mid-seventh century. Because these Egyptian Copts were Christian, to the Muslim Egyptians, they essentially remained guests in the own ancient house. 
Egyptian Christians have historically often borne the brunt of Muslim rage, ending in the murder of Copts and the destruction of their churches. This formally contradicts Islamic Shar'ia law, according to which, Christians are allowed to live under Islamic rule, albeit as second-class citizens. Even so, violence against Christians, Jews, Hindus, and other minorities -- in Iraq, Yemen, Bangladesh and other Muslim countries -- has been has been part and parcel of Islamic culture for centuries.
During the first few days of the Tahrir Square, during demonstrations against Mubarak, some Muslims demonstrators protected the Christians as they prayed at the square. Shortly after the public Christian prayers, however, the wrath of many Egyptian Muslims returned; they turned on the Christians, even though the Christians had never, of course, been the cause of the Egyptian people's anger towards the Mubarak regime. The anti-Christian and anti-Semitic attitudes displayed by large numbers of Egypt's Muslims from all sections of society -- peasants, city dwellers, the military, and Muslim intellectuals, and from the Egyptian religious establishment -- have been involved in a violence that stems from Islamic culture and that fosters anti-Christian, anti-Jewish, anti-Hindu and anti-"other" sentiments.
Although many Muslims may say they adopt modern ideas such as democracy, freedom, and human rights, the question remains how deeply these concepts have permeated a habitual way of thinking. So many of our Muslim government and political interlocutors cloak their thoughts in words familiar and soothing to the West. Our government leaders and bureaucrats therefore believe -- and want us to believe -- that these observant people are like us. Sadly, we are all too willing to accept their words at face value. We cite Islamic religious law as if we understand it better than they do -- and as if to reassure ourselves that these Muslims actually do accept our way of looking at the world. Our government officials and academics often go to great lengths to find fatwas emphasizing that Christians, Jews, and Muslims can co-exist peacefully; while formally true according to Islamic law, however, this "co-existence" only happens where Islam rules, and Christians, Jews, and others live as second class citizens.
Today, almost any bearded individual who calls himself a Sheikh can issue fatwas; and can easily find fatwas to support almost anything. It seems as though these Sheikhs now have more influence than traditionally-trained Muslim religious leaders, and currently constitute what is regarded as Islamic culture.
It might be helpful to ask why we refuse to see Muslim culture for what it is. The answer, unfortunately, is that if we did, we would then have to re-think the ways we deal with leaders from Muslim countries in ways our policy establishment is simply not prepared to do. If we stopped deluding ourselves, we might have to ask ourselves whether the Saudis can really be our allies; their long term goals are so inimical to ours. This view does not necessarily mean that our interests always diverge. The Saudis, we, and even Israel, for example share similar views on how dangerous the Iranian regime is to our interests. But these are just short-term interests. In the long term, it is clear from the abundant writings produced by the Saudis, Salafis and other Wahhabis that they want to destroy both our culture and us.
If we were to recognize this reality, we would no longer we able to hide behind the misnomer that Islam is a religion of peace, and that Islamic culture -- which stems from the Islamic religion -- and the West cannot in the long run peacefully co-exist. If we were to recognize this reality, our whole outlook on and policy towards the Islamic world would have to change. Are we prepared to do that?
 This conclusion is based on many decades of conversations with Turks, Iranians, and Arabs. See also http://www.theblaze.com/stories/2012/09/21/why-do-they-hate-us-its-a-pretty-long-list/, and http://www.atimes.com/atimes/Middle_East/IJ23Ak01.html.
 See Bernard Lewis, "The Return of Islam"
 On these terms, see https://www.gatestoneinstitute.org/2572/brotherhood-in-islam
 "People of the Book" (in Arabic Ahl al-Kitab) is defined as fellow monotheists which received a revelation from God before the Muslim prophet Muhammad lived.
 For the classic definition of dhimmi, see http://spa.qibla.com/issue_view.asp?HD=7&ID=12588&CATE=1430
 See http://www.aina.org/news/20101123195608.htm, and http://www.refworld.org/cgi-bin/texis/vtx/rwmain?page=topic&tocid=4565c2253e&toid=4565c25f49d&publisher=IWPR&type=&coi=IRQ&docid=4b138dad29&skip=0