As one might suspect, part of the reason for this is that the first half of The End of Faith is far stronger than the second half. The first four chapters, Reason in Exile, The Nature of Belief, In the Shadow of God, and The Problem with Islam, present as stark and compelling argument for atheism as any I've read, dealing with the decline in rational thought since the heights of The Enlightenment, what's wrong with religion in general, the horrors that religion has wrought on humanity, and the particular perversion which is Islam (the six solid pages of "fatwa-justifying" quotes from the Koran is chilling enough). As much as I'd like to pad out this review with arch quotes from the text, I had to give up on that idea after only a few pages, as sentence after sentence screamed to be quoted, and it was obvious that I was not going to be able to bookmark "highlights" ... it's just that amazing.
However, Harris, while not weakening his polemics, changes directions in the second half. While the first half stands as a "statement for the ages", much of the second has, even now, a feeling of being "soon to be dated", especially the chapter West of Eden where he addresses how religion (and, obviously, fundamentalist Christianity) is corrupting Western, and especially American, society and government. From here the book turns into more of a "morality/psychology" survey, first with A Science of Good and Evil, and then "Experiments in Consciousness", which is (as one would guess) a look at possible ways of transcending religion.
Personally, I wish he'd done two books ... rounding out the first half with a chapter or two of more "rallying the troops" (and he is, with me, certainly "preaching to the choir" there), and then presenting a more "newagey" look at "what's wrong with religion, and what to do about it" as a second title.
To be honest, Harris significantly undercuts himself in that last chapter, as he reveals that he is a meditator and a quasi-Buddhist practitioner. Now, while Buddhism is, by definition a "non-theistic" creed, it is certainly framed, both within and without, as a religion, so advocating practices and approaches associated with that creates a certain dissonance in his allies, and provides a huge "stick" with which his enemies can attack the rest of his thesis. I mean, it is one thing to hold out Jainism (as other atheists frequently do) as a "harmless" and/or relatively "sensible" religion, and another to be advocating "the wisdom of the east" as a solution to the problem of religion. While his point in this is quite well taken (that Western philosophy and the accompanying monotheisms have produced less truly introspective material than Islam has quotes supporting it being "the religion of peace"), it does read like "a confusing eruption of speculative philosophy" in context.
Had Harris done two books, I would be standing on the street corner handing out copies of the first, which is not to say that the second is weak or wrong or not extremely worthwhile; but I do feel it's unfortunate that this plays out the way it does. Certainly, religious fundamentalists will use the latter material as a straw man to attack the earlier, a situation for which Harris "leaves the door open". Of course, I also feel bad about bringing this up as a criticism, as nearly everything that he brings up in that final chapter I (who have also studied Buddhism and various other Eastern systems) heartily agree with.
All that being said, I highly recommend getting a copy of The End of Faith! It's in print (so will be at the local bookstore), is very reasonably priced at $13.95 (Amazon has it at 20% off), and really deserves to be part of the culture's basic discussion.