The thing that I was mulling over was the fact that so often in stories, people use a setting in the future to get rid of some aspect of present-day culture that they dislike (contrariwise, they often highlight or exaggerate things they dislike--that's the dystopian instinct), and one such thing is present-day religion. And yet, religion won't easily just vanish. And yeah, I agree that lots of stories treat religion poorly (in the sense of simplistically).