Despite wild speculation that Superman is a humanist, he is apparently Methodist (or Raoist, if he’s feeling particularly Kryptonian). Batman’s upbringing was either Catholic or Episcopalian; in either case, he’s definitely lapsed, and “there is universal agreement that the character is not an active churchgoer in any faith.”
Who are the atheists? Apparently: Mr. Terrific, the Savage Dragon, Booster Gold, Quasar, Dreadstar, Vivisector, Supershock, and others. Not exactly household names. Although it’s interesting to see Wolverine described as “sometimes atheist” and Iron Man as “futurist; technologist; mostly secular.”
And it turns out there actually is a comic book hero called The Atheist, although it seems to have been something of a missed opportunity: according to Jeff Swenson over at American Humanist, the creator Phil Hester “squandered a perfectly good idea — the idea of a genius black atheist who encounters cults and battles pseudoscience — and turns it into a dead-take-possession-of-the-living rehash of countless horror movies.” A shame. It would have been nice to see a fresh take on the debunker-as-hero, picking up where Sherlock Holmes and Scooby Doo left off.
Perhaps someone should take this idea and run with it: