At its heart, the book is arguing against Faith. His starting point is Islamic terrorism, which he argues can only be understood in the context of faith--without the religious beliefs underpinning these people's lives, without the certainty they have in both the righteousness of their cause and the eternal reward they will earn, recruiting for suicide bombing missions would be awfully hard. 
 Part of his argument, though, is that contrary to what we typically say, the problem isn't just a few extremists. This plays out in two ways. In the first place, he looks squarely at Islam. While it may be true that it's not every Muslim who is lining up for suicide bombing missions, it's also true that there are a lot of passages in the Koran which enjoin hatred or at least disdain for the infidel and a lot of other passages that glorify armed conflict against said infidels. To provide weight to this argument, he not only quotes extensively from the Koran, but he also cites a worldwide poll of Muslims that seems to find is an awful lot of tacit support for the suicide bombers. 
 Harris does not only blame Islam, though. He also targets, in the West, the way that we treat religion in public discourse: that is, with kid gloves. If someone speaks of their religious faith in public, then that's it, end of discussion. There is not allowed to be any questioning or criticism of that faith. This kind of "respect" for faith gives cover to the extremists. Also, in a democracy, such "respect" has real, dangerous consequences. Look, for instance, at the results we've gotten with the Bush administration: policies and political appointments based on religion. Harris examines a number of ways that this has played out in the U.S. At its heart, religion is making claims about the world--about how it is and how it should be. These claims should be open to scrutiny and debate the same way that scientific claims are. If "God" may not be as easy to "prove" or "disprove" as many ideas of science, there is still evidence to be marshaled on either side, particularly when a particular faith is on the line. A claim for the existence of God is difficult to disprove, but a claim for a divine, inerrant Bible, for instance, is not. 
 Harris is not, in the end, dismissive of spirituality as such. He is quite respectful of the idea that there is something that is probably best called a "spiritual" side to life, even in the absence of God. Not only is there room for such a thing, Harris finds spiritual experiences and spiritual inquiry quite valuable. 
 Harris's discussion can get quite detailed, and he shunts at least some of the discussion of philosophy, neuroscience, and other deeper discussions into the endnotes. At times, these end notes can be quite lengthy, and this was probably a good choice--go deeper if you want (there's also a bibliography) or stick with the main points of the discussion. 
 There are certainly points that readers will find questionable or even objectionable, but this is an interesting, thought-provoking, well-argued book.