Mr. Terrific is a member of the DC Universe's Justice Society of America. Mr. Terrific is an atheist.
In the 1940s, the JSA had a member called the Spectre. The Spectre was and is God's agent of vengeance on Earth. He is a supremely powerful cosmic force and on occasions when he has gone rogue, he has posed a threat to the entire DC Universe.
One time, Superman died, and then he came back.
Green Arrow did the same thing. His soul was actually retrieved from the afterlife by Green Lantern, who, at the time, was acting as the human host for the Spectre.
Once, there was a fallen angel on the Justice League of America, called Zauriel. When he fell to Earth, he was chased by other, evil angels, whom the Justice League fought and defeated. Magic-wielding heroes and villains have often had dealings with Neron, an actual demon from Hell. Blue Devil and Kid Devil are active heroes at the moment; when they enter churches, their skin burns. There's another hero, Ragman, whose powers are drawn from the souls of repentant sinners.
Wonder Woman regularly interacts with actual ancient Greek gods.
Does it make sense to believe that there are no gods, when Solomon, Hercules, Atlas, Zeus, Achilles and Mercury grant Captain Marvel power whenever he speaks the word "Shazam"? When the Judeo-Christian God ("the Presence") has been explicitly acknowledged to be a part of the DC Universe?
What we find is that we have to alter our definition of the word "god" for a statement of atheism to make sense in a comic book universe. If a god is a being of tremendous power, then unquestionably, gods do exist in the DCU. Any Kryptonian qualifies, if sheer strength is any measure of godhood. So that can't be it.
If a god is a being which is holy/sacred/divine/worthy of worship, either you have a circular definition (because something is only holy/sacred/divine/worthy of worship if a god says it is) or one can decide for oneself what is or is not holy, and "holiness" and "divinity" are just words. In reality, as in the DCU, power does not, in and of itself, deserve worship. In fact, even overt, benevolent action may only earn one respect and credit, not worship at all.
A better definition might be that a god is something which is both powerful and inexplicable. Unknowable, untouchable, ineffable. Here is where we can get to a definition of atheism which works both in reality and in a comic book universe: a disbelief in the inexplicable, the belief that everything in the universe operates on rules, so-called "gods" included.
Magic incontrovertibly works in the DC Universe. Magic can be duplicated in laboratory conditions. It is a sticky process, prone to quirks and irritability and it can get worn out through overuse. There is old magic and new magic and they work differently. The rules of magic can change. Magic can run out. But magic is subject to rules. It can be and is studied by magicians. There are books about magic. That means that magic, even if it is magical, is a science. It is a part of science.
If you can punch Ares, god of war, on the arm, then he must have an arm which can be studied. If your prayer works nine times out of ten, there must be someone or something answering it – maybe you have psychic powers and you're answering it yourself. That mechanism can be studied. If the Spectre appears to have tremendous unstoppable power, because he was granted that power by God, all you have done is assigned the name "God" to what is simply the most powerful thing inside or outside of the universe.
The fact that people can return from the dead may well prove that there is an afterlife. It may prove that the notionally "supernatural" exists. But it doesn't necessarily fill a sufficiently sceptical onlooker with fear or shock him into obedience. To an atheist, it is just another phenomenon in the world. To an atheist scientist, it is just another phenomenon which demands study. Just because the rules really do work like the old myths said they should doesn't change anything. The DC Universe has additional rules. It has extra features which don't exist in reality. But they're there, and they happen. Therefore, they can be studied and exploited. This is a rational stance to take. It's the thinking person's stance to take. If praying to Hera can be proven to actually grant additional strength, praying to Hera is a logical move, not one of faith.
There are other DCU characters with similar opinions. Doctor Thirteen is a character who flatly denies belief in any apparently supernatural event and desperately seeks a logical explanation within conventional science – this is primarily played for comic effect. He has every right to his scepticism, but tends to take it too far when he could simply accept the new rules and work with them.
Batman has been written in different ways by many people. He's dealt with enough supernatural and occult heroes and villains that it's logical that he would believe in an afterlife where, for example, his parents are waiting, but he is a paranoid and scientific man who understandably distrusts concepts so slippery as magic and spirit. If nothing else, Batman would be reluctant to entrust his life to them when perfectly good conventional science can support him instead. But if he was on the same side as Captain Marvel or Wonder Woman, he would trust them, as people and teammates.
In effect, atheism is a lack of faith, that is to say, a lack of belief in anything for which there isn't hard evidence. Just because there is hard evidence for some very strange things in comic book universes doesn't change that. In fact, it makes atheism an even more logical stance to take. If we have people who can fly under their own power, why shouldn't they be able to pretend to walk on water? Or raise the dead? What's to stop any ancient miracle being an early mutant or metahuman working powers which the people of the time never understood?
Scepticism is always healthy.
Comic book characters' religious affiliations: http://www.adherents.com/lit/comics/comic_book_religion.html