I think he pretty much answered that, Generator - he believes, for his own personal reasons (posssibly inexplicable, but then, so many personal reasons are) that religion is a more important, or perhaps more sacred (no pun intended) belief, and that it shouldn't be exploited.
The way I see it, religion is the last great divider, you still see people widely segregated based on religion or sect, and many people in their own minds draw distinctions between relgions and sects (Catholics have a guilt complex, Hillsongers are all freaks etc.) without any feeling of guilt. It seems to me that religious prejudice is the only form of "acceptable" prejudice in our society, which means that it can be wielded very easily, and guilt-free, by those in power. As somebody (was it you?) said, you can call the atheists baby-killers, and the fundies unenlightened zealots, and not only will it be considered virtually acceptable, a hell of a lot of people will agree with you.