There's also evidence that Batman is a lapsed Episcopalian. Some people have even tried to explain it as Episcopal on his father's side and Catholic on his mother's side, although Frank Miller, who wrote the comic you mentioned, is a Batman as a lapsed Catholic guy. I think he's just projecting a little bit of Daredevil into the character, myself.
But most writers write Batman as so logical that even when presented with concrete proof of gods and God, he considers it another scientific, explainable phenomenon and not something spiritual to worship. Batman has proof, but he doesn't have faith.
There's no need to talk about the Smurfs' communism, they aren't atheist because they live in what seems close to a pure communist society. They're atheist because they seem to have no gods, not even any mythology from what I can tell.
Chuck tends to do that a lot, actually. He's a good writer and it leads to some interesting takes on the characters, but it's not something you can expect to stick when the next writer takes over.