Studies that show that religion is just the result of intuitive thinking have become a very tempting carrot to more outspoken skeptics - the ones who compare religion with so much vapid self-delusion. The unspoken (and frequently spoken) conclusion being that "if you just thought about it, you'd never believe it."
There is, however, one area in which the roles are oddly reversed: morality.
The religious have a very rational grounding for their belief in morality: If the universe has a Designer, then morality is a function of design. Free-will, choice, justice, and intelligibility all flow from this concept of designer and design. Atheists, on the other hand, tend to use intuition as the basis for morality.