So...when I wrote my query letter and then submitted it for critique at Absolute Write, I expected a few people to object to the general content of my book. Vladimir Nabokov once said that there were three taboos in American publishing: incest, interracial marriage, and "the total atheist who lives a happy and useful life, and dies in his sleep at the age of 106."
Happily, interracial marriage is no longer the taboo it was in the 1950s. Incest will always remain a taboo -- or at least I predict it will remain taboo in my lifetime. Who knows what the future might hold. As for the third publishing taboo, obviously Nabokov was being hyperbolic when he described that scenario. A book about a happy, useful person who never has any troubles and dies in his sleep is boring, and boring will always be verboten in publishing. But the point he was trying to make was sound, and unlike interracial marriage, a book which portrays atheism as a solution to a problem, or at least as something that's okay, something that doesn't need to be fixed, is still going to have a tough time getting off the ground.
That doesn't mean I think my book is doomed. It merely needs to meet the right agent and editor, and I then I think it has quite a good shot of selling well. But finding the right people to work with this book may be difficult, and my experience with my query letter on AW points out why.