Sam Harris’s The End of Faith is an assault upon religion, blind faith, and fundamentalist violence. However, clear thinking Christians have little to fear from Harris’s social critique.
The majority of the book is an exposition of the evils, real or imagined, produced by religion. Harris discusses current atrocities, including September 11 and suicide bombings in Israel, as well as past atrocities, including the Inquisition and the Salem Witch Trials. This leads to the natural question- if Harris (an atheist) is so critical of religious horrors, how can he explain the atheistic regimes of Hitler, Stalin, Mao, and Pol Pot, which collectively were responsible for millions of deaths? Harris claims that, while they may not have been explicitly religious, these evil regimes were the result of poor thinking. He states in his afterword-
“While some of the most despicable political movements in human history have been explicitly irreligious, they were not especially rational. The public pronouncements of these regimes have been mere litanies of delusion- about race, economics, national identity, the march of history, or the moral dangers of intellectualism.” 
Thus, we see that The End of Faith does not really support atheism or oppose religion, it simply supports reason and opposes blind faith. Otherwise, his critique of religion is completely arbitrary, as he admits in this quoted passage that the real enemy is not simply religious faith, but irrationality itself. Thus, Harris needs to demonstrate that Christianity inherently necessitates irrational faith if he wishes to demonstrate that it should be rejected. Throughout the book, Harris merely assumes that so-called “fundamentalist” Christians can only exist through blind faith, but his assumption is both unproven and incorrect. Despite railing on about the supposed irrationality of religion, Harris never once deals with any of the arguments offered by Christians either historically or in the present day. There is no critique of the Cosmological Argument, no consideration of the evidence for the empty tomb, no critique of biblical passages or doctrines. Harris simply assumes that Christianity requires blind faith, argues that blind faith is both stupid and dangerous, and declares victory. The problem is that he has never shown that Christianity requires blind faith.
The other problem with Harris’s approach is a common one- he assumes that the misdeeds of religious followers invalidates the religion itself. This is simply a bad argument, as I show in my article on the subject here.
Thus, the majority of Harris’s book is simply not relevant for intelligent Christians. Surprisingly, however, there is some value in The End of Faith. For example, he discusses morality and makes a good case for charitable giving, and discusses politics and law, and makes a good case for the legalization of (some) drugs as a matter of public policy. However, as a critique of religion in general, and Christianity in particular, The End of Faith fails quite miserably.