A bit of the skepticality-of-the-West in Islam was hinted at through the tragedy of the corruption of Islam by wealth early in it's existence - the notion of what constitutes corruption, the relation of piety to virtue, etc. I find myself placed, as I so often have been since striving to understand history, in an area where there really arn't good guys and nobody aligns well with my values. I'll greatly simplify the situation and mention that Islam under Mohammad was a simple faith stressing a moderate disinterest in material happiness, a strong dislike of wealth, rejection of pomp, etc. For what this was, it was not extreme - people had music, partook of some pleasures outside the faith (good food, etc), took care of each other, were not suspicious of each other's happiness, had a lively society without strong gender segregation, and were not puritan. After Mohammad's death, the community was pulled in various directions by the four Caliphs, the second of which, Omar, was legitimately closer to being puritan, and the third of which, Othman, allowed private accumulation of wealth and pomp. After the fourth Caliph, Islam soom became a military force under a monarchy, later to divide over the political struggles over its direction. The book draws parallels to both the Wahabis and the Muslim Brotherhood as movements to reverse the modernisation and accomodation to the west and go back to their views of pure Islam.
I can empathise a little bit more with Wahabis and the Muslim Brotherhood given who their enemies are and how they frame them, although their break (particularly the Wahabis) with what I know of the prophet seems prominent (not that they would take the word of an atheist socialist as being particularly convincing on this matter, and their break from the subsequent developed traditions of Fiqh and scholarship could be justified as a skepticism of the legalism that I now understand to have been warned about by the prophet (note that I call him as such because of notational convenience and to aid in helping make their viewpoint more transparent - I don't believe in prophesy or gods, as any reader will well know). If the tragedy of humans being unable to maintain the goodness of early Islam is to be taken seriously, the Shi'a fixation with geneaology of the prophet and insistence on religious prominence for his descendants, eventually to fall into the simplifying notions of some of these spiritual leaders becoming hidden from the world to return someday becames a way to avoid looking that reality in the face - piety or virtue of any sort is difficult at large scales and is easily lost. Wahabis and Muslim Brotherhoods could easily see in the world the wealth-obsessed nonegalitarian nature of modern Muslim nations as diseases to be cut away from the body of Islam (and in that bare judgement they are not heretical, although the Wahabi at least are hypocrates for their ties to the House of Saud).
Do we have to take that dualism? Is it tempting? I am tempted - given a choice between pomp/wealth/kingdom/business and piety/asceticism/egality/virtue, I am inclined towards the second in most ways, the issue being that I view piety, asceticism, and virtue rather differently. The way the decision is framed isn't one I like, and this framing is embedded in the biggest sides of the dispute in the region. I believe in goodness without gods, a different set of virtues, and asceticism in a different sense. Asceticism as it has existed is the limiting of focus on material comforts in order to focus on something else - in the case of Islam, it is one's relationship with god. In my case, it is culture and the public good itself - I would pare away different things, including the wealth, pomp, and privilege, considering these to be products of human faults, but the better focus of energy should be the pursuit of knowledge, cultural production, and personal growth. My secular notion of virtues and values are not exactly what Muslim radicals are struggling against (although they very well might), but it is also not what Western civilisation is entirely about - our civilisation is as corrupt and ugly in most respects as their homegrown human failings, and the radical groups identify in us their own failings (they are our failings too, if we accept something vaguely like my value system as "the" ideal of western civilisation). Particularly as Americans, we've celebrated shallow materialism, wealth, mass-produced styrofoam lives, lack of care for each other in the name of individualism, and lack of personal development for Western Civilisation to the extent that our inner cultural struggle cannot help but remind muslims of their own failings relative to their virtues, and they are an easy distraction from their own failings - it is far easier to blame others for their corruption than to remain affixed to theirs.
It is saddening to me that as seculars we have not built much of a system to compete for the heart of society. An atheist identity is not a substitute for everything competing philosophies (including faiths) offer. In our rejection of socialism, we either made a mistake, or we gave up too much (I hold the former to be true, although I am prepared to argue for the latter as well) - replacing any notion of virtue with the notion that a somewhat constrained individualist greed produces a good society is a harsh mistake.
I cannot blame those that would reject this empty consumerist reality that some parts of the west push onto the world. The Neoconservatives and objectivists, with their intent to spread this reality of weak democracy, strong markets, and dead culture to the world aim humanity for the gutter. Our civilisation is a strange multiheaded beast and until and unless we can purge it of both the emptiness of consumerist nihilism and the ill-fit of christianity, our defense of it should be nuanced and understanding.
Of course, under the umbrella of Islam there are many cultures, ideas, and the like, and we are not compelled to like them either, particularly those grossly repugnant to our values. Their belief in a god and treatment of belief or lack in others is a division, their illiberalism is another. Wanting or allowing them to become just like us as we are now would be a terrible mistake though.
PZ Meyers, while a good professor (I have learned quite a bit of assorted biology from reading his blog), is a troll on the topic of atheism. It is not that I think a hardline position on atheism is unwarranted, but a kneejerk one is. There exist people who believe there to be no god, that the world could be better off without religion, and are devoted to carefully guiding humanity to what we hold to be higher moral/ethical systems. We can hold a firm atheist identity, not claim that "all that matters is what people do rather than what they believe", and guard against blurring our identity with liberal religious folk when we find common cause or socially mingle. We do not need to be rude to religious people, call them idiots, refuse solidarity on common ground, a-priori avoid friendships, or be unfair. PZ Meyers fails most of these and breeds ugliness on his blog with the circus atmosphere (gee, who shall I block today? Let's vote!). In his actions, he hurts the cause with zealotry, ensures our level of thoughtfulness remains very low (and so hurts our philosophy), and distracts us from treating other people inside and outside the movement well. Richard Dawkins, by comparison, is much more polite and thoughtful (even if he's not as thoughtful as I'd like on rare occasions - I'm not as thoughtful as I'd like on some occasions either, not that I speak on these matters nearly as much).
Somewhat related, here is a bit of back-and-forth which PZ commented on that I particularly object to - their characterisation of science is that of a partisian rather than a thinker, and they don't get down to what science is as an institution or the philosophies it uses. For those of us who think science is a good way to understand the nature of things, there are reasons why we do so - we have learned to see the distortions in our subjective experience and how we build frameworks to understand the world, and science as an institution helps us reduce/limit those distortions on both an individual and group level. Science also is generally validated by both the data we accumulate under its umbrella and the engineering it permits - these are not unassailable reasons for science, but they are very strong and at least in areas where they function, we do not have other drastically different sets of means that work better. Incremental improvements to science have been rolled into science - the embrace of statistics, the maturing of disciplines, the growth of peer review and journals, simulations and roboticisations, all of these have developed as the social institution of science has shifted over the centuries. The materialism of science has not always been a core tenet, and more importantly it is only methodological in necessity. Science as a discipline assumes the world to to be material because we have no way to investigate the realms of alternative frameworks (If we ever found a way, we would incorporate them). This by necessity blinds us to possibilities that violate that assumption. Likewise, Occam's razor (to the nuanced extent that it is part of science), the conditions of what we can observe from our temporal and physical vantage, and our ability or lack thereof to intuitively wrap our heads around various ideas potentially limit what we can see in science. If we are to be thoughtful about science, we must admit and accept these limits.
Those of us who wish to push things further must start our arguments from there and realise that they are not part of science itself. Practices recognisable as science have existed for many years, practiced by Muslims, Christians, believers of many other things. These should be recognised as science - it may be a tenable position (and I believe it is) to say that the success of methodological materialism makes a good case for philosophical materialism, but that is not an argument intrinsic to science - it is a philosophical argument and cannot be demanded of those who practice science on grounds of heresy towards the field.
An undue focus on "the enemy" makes our philosophy shallow. It is a strange revisionism to consider science under the revisionist's light that would deny most of the existence of science as being incompatible with other frameworks with which they know it preexisted (just as strange as those who would taint all of capitalism and perhaps all of human civilisation that was not lassiez-faire as "fascist communism") - it calls a modern creation to be the only true form of something that has existed for a very long time. That's not what honest and careful discussion looks like.