Actually, the context of the Marvel Universe makes it easier to be an atheist, not harder. Yes, the gods of pagan religions may have turned out to be real, but... should people worship them?
People seek divine explanations for the things that can't be explained by rational and mundane ways. People do not worship things that can be explained: once we learned about the water cycle we ceased praying to the gods for rain. And there is much less chance to worship things that can be replicated by oneself, without divine intervention.
Let's consider the best noteworthy example, Thor and the "gods" of Asgard. What is there to them that can make them divine and worthy of worship? What aspect of them can not be explained, or replicated by "mere mortals"? (and with that I mean "not divine", so it includes both humans and mutants, inhumans, aliens, etc.) The Odin-Force? There are several "forces" that can empower a host, such as the Phoenix Force or the cosmic power. They come from another dimension? Big deal. So does Blastaar, Annihilus, and others. Magic? Dr. Strange, a human, learned it all and is the master of all magic users, just by studying books. Heimdall can see everything? The watcher, an alien, can do that with his innate power. Super strength? We have a Hulk. They have awesome weapons? We have a Stark... and he once worked in their forgery, and made even better ones.
Even complete and absolute omnipotence can be replicated if you have a cosmic cube or the infinity stones.