"Defined by" is an odd way to phrase it. There are atheist characters in comics, but to say they're "defined" by it is a different matter. Frankly, pretty much any character, if they were defined by their religion - rather than simply having it as one element in their character among many others - would be pretty boring, imo.
Anyway, Mr. Terrific is probably the most well-known atheist in comics.
He is, though unlike Krisblaze being a complete tard, he isnt defined by it.
Other characters you may want to check are Anarky, Booster Gold, and Starman Ted Knight.
How about Doctor Thirteen? While he's not exactly 'all about atheism', his scepticism would put him in the ballpark for the sort of character you're talking about. (And to be honest he's a bit more interesting than Dr Manhattan, who does mind-bending stuff but manages to be as dull as hell as a character)
Yeah, and I dunno if the Source is general knowledge for all DC heroes/villains. But Marvel and DC make it really hard to be atheistic with their rather explicit deities.
I'd love to see Doom become a solipsist because of the events of Secret Wars. Of anyone, he's the most likely to actually have reason to believe he is and will always be God.