Isn't this inherent in the whole fantasy concept? You start writing about a world wherein magic of some kind does exist; worldbuilding demands also that faith exists; at some point, you are going to wonder whether or not that faith is based on something more than wishful thinking. Where dragons are real, why would the gods not be?

And if you have unbelievers, there are better things to do than shun them. They can't be let walk blindly through the novel, where veils exist to be dropped and epiphanies enacted.