Basically, McGrath seemed to me to be asking the wrong question. His argument identifies "atheism" as a collective identity more than is really warranted by his own evidence; towards the end he seems to almost criticize atheists for not being as well organised as the Church, which sort of misses the point. More widely, he never makes it clear whose atheism or belief is under discussion, though I felt that in the present day he really just means Oxford dons. Non-Christian faiths are barely mentioned; there is an anecdote about the triumph of Christianity in Korea in the 20th century which simply does not refer to other religions practised by Koreans. This really isn't good enough.
The internal structure puzzled me as well. I would have preferred a more strictly chronological organisation. But instead we have a chapter on Feuerbach, Marx and Freud, followed by one on the sciences post-Darwin, followed by an examination of atheism in classic literature from the Enlightenment on (that last being one of the better chapters in the book). It is as if Freud knew nothing of Darwin, and Darwin knew nothing of Keats. (I confess I had not preeviously heard of Feuerbach, but that may just be my ignorance.)
Other irritations: James II was not Charles II's son (p 14). I was surprised to read (p 264-265) that "The role of religion in creating and sustaining communal identity has been known for some considerable time, and has become increasingly important since about 1965"; I think it's just possible that religion played an important role in creating and sustaining communal identity for quite a long time prior to that date.
I suspect that this book was intended to be in part a rebuttal to Richard Dawkins, who is very briefly dissected, but unfortunately it is too full of its own complacency to be effective.