I have to admit up front that I haven't read any of the works of the "New Atheist" authors who are the prime target of D'Souza's modern-day stab at a Christian apologetic on the order of C.S. Lewis' famous works. Taken strictly as a face-value argument that Christianity provides a more coherent and satisfying explanation for the natural world, human behavior, and human origins than atheism, D'Souza's work has a number of fairly obvious holes. Most of these relate to the fact that, while a number of his points in favor of religious belief score effectively, they might not convince a skeptic that a belief in Christianity necessarily must follow. For example, I agree with him that the "Big Bang" theory of the universe's origin is an exceptionally strong argument for some kind of "prime mover." Jumping from that to a belief in Christian doctrine is a "leap of faith" which some may not be able to make. Likewise, D'Souza makes good use of Immanuel Kant (and provides a nice refresher course in the ideas of the great philosopher, besides) in arguing that there are limits to what human reason can grasp, but is this a positive result arguing for the specific identity of what we can't grasp? Generally speaking, D'Souza is better at parrying the slings and arrows of atheist opponents than at racking up scoring thrusts of his own. As a Christian, that's not to say that I don't appreciate his efforts.
Where I believe that D'Souza is on absolutely solid ground is when he attacks the atheist "meme" that Christianity is guilty of uniquely monstrous historical crimes. Crimes there certainly were, but to try to explain away the mass murders by the totalitarian movements of the 20th century as some sort of indirect manifestation of the religious impulse, as some atheist writers have tried to do, is downright dishonest at its heart. Fascism and Communism were a perverted, secularized version of the religious impulse, rather than the real thing itself, and the scale of magnitude was immensely larger. Islamic radicalism is a sort of monstrous mutation of an actual religious faith with political radicalism and, as such, has provided a lot of the fuel for the atheist bandwagon in recent years. Christianity, however, continues to receive the lion's share of cultural criticism. While his arguments certainly could have been stronger, D'Souza's book repays reading by believers and nonbelievers of all stripes.