Of the many aspects of Mormonism that make it so incredibly fascinating is the fact that it was gettin' started recently enough that there's such a rich record of its origins, which, unfortunately for Mormons, this don't make for the most flattering picture. It also makes various claims in the Book of Mormon eminently falsifiable, like the fact that all Native Americans are descended from the Israelites (DNA sequencing has shown their last common ancestor to be much older).
The book's anti-religious argument (which is subtle, but I think, pervasive) goes further. In one of the book's most poignant scenes, two psychologists duel it out on the witness stand, giving conflicting testimony over whether the defendant in a murder trial should be considered insane for claiming to have received revelations directly from God—in this case, revelations ordering the murder itself. The prosecution witness makes the obvious point that religious people claiming to communicate directly with God are all over the place; in addition, people of every religious denomination subscribe to beliefs that can hardly be justified based on evidence; should we consider all of them crazy? But if we don't think the murderer in this case is insane, does that mean we allow for normal, functioning sane people to have consistently detailed delusions?
The whole book makes a great argument against religious faith by inconsistent revelations; throughout the book there are dozens of people claiming to be the one true Mormon prophet, communicating regularly and directly with God, and even willing to stake their lives on their prophethood. But their revelations are all wildly inconsistent, flatly contradictory, and in too many instances, crazy illegal. In the end it's an argument about human nature: we are quick to put faith in ourselves and our own delusions.
Interestingly a lot of people on Amazon seem to take issue with the book's message, which is to say they accuse it of anti-Mormon bias. Of course I'm not historian, so I don't really know whether the book is biased or not, but I think these people are confusing argument with bias. No, the book doesn't paint a flattering picture of Mormonism or religion, but I think that's kinda the point.
Another big theme of the book is polygamy and its role (which is a big fat one) in the LDS and fundamentalist LDS churches past and present, especially leading up to the murders mentioned above. I mean some people really get carried away with the polygamy thing. Krakauer fails to mention and investigate an obvious mathematical consequence of fundamentalist mormons' practice of polygamy (actually polygyny): unmarried, sexually frustrated men. No wonder these communities tend to fracture often! I assume that "plural marriage" is in practice a luxury reserved only for the well-connected and powerful in these fundamentalist communities. Still, it doesn't take too many men with 20 wives in a small community of 5,000 or so to really screw with gender ratios. It's no surprise that the powerful men end up taking younger and younger women as wives, because these communities must be continuously short for eligible women. Krakauer argues, by implication, that polygamy leads to pedophilia through a general lack of respect for women and their choices, but the connection is in fact much more direct.