Think of the old cliché about the mind being 'an excellent servant but a terrible master'. This, like many clichés, so lame & banal on the surface, actually expresses a great & terrible truth.
They're probably even more repulsive than atheists, at least to most of us here, but the fact is that religious dogmatists' problem is exactly the same as the story's atheist's— arrogance, blind certainty, a closed-mindedness that's like an imprisonment so complete that the prisoner doesn't even know he's locked up.
Learning how to think really means learning how to exercise some control over how and what you think. It means being conscious and aware enough to choose what you pay attention to and to chose how you construct meaning from experience.