It's relatively common to have a character who openly acknowledges the existence of beings of great power, but refuses to accept their divinity (either because he believes them to be Sufficiently Advanced Aliens using technological trickery, or because he differentiates between a 'real' god and a supernatural being that is merely very powerful). Sometimes this is a direct attempt to discredit science by comparing it to religion: instead of using the scientific method, as a scientist does, the strawman atheist relies himself on a devout faith - in this case a faith that ' science' holds all the answers, despite obvious proof to the contrary. Sometimes the character himself is a god (typically a loony one).

Maybe they don't believe in the gods at all and are totally nuts, maybe they're completely in denial about the existence of gods, or maybe they're feigning disbelief in hopes of ending their worship and bringing about some kind of Götterdämmerung or whatever. A self-styled hardline atheist that just happens to live in a high fantasy setting brimming with both huge pantheons of gods rampaging around the landscape constantly causing all sorts of things to happen, and the worshipers that pray to (and immediately hear back from) said pantheons of rampaging deities. While some authors do this as an honest philosophical exercise, it's almost always Played for Laughs. Atheism in a clockwork universe ostensibly overseen by a completely non-interventionist divinity is one thing, but what about a world that's practically the playground of the mythic forces that created it?

Flat earth society joke