Mulder and Scully didn't so much represent "supernatural" vs "logic, science, and reason" as they did paranormal vs mundane. A whole lot of the things Mulder thought were happening were things that could have had a naturalistic explanation that you could do science to understand if they actually were happening at all —they were just extraordinary things the likes of which would require extraordinary evidence to accept. Scully was rightly hesitant to accept such things without extraordinary evidence, but then, she also accepted supernatural things that are widely accepted and considered mundane, normal beliefs by society — her religious beliefs.
That was actually my favorite thing about the show and something I thought, around (I think it was) the season seven finale, they were going to shift to exploring: the paranormalization of religion. Looking at religious beliefs as just as weird and extraordinary as the aliens and monsters Mulder was always on about, and possibly actually connected to those very same things, but at the same time all of it still rationally, naturalistically, scientifically explainable. But of course that would never fly, especially on Fox, and they chickened out and ignored it aside from some vague allusions to Mulder being Alien Jesus or something in the terrible last two seasons.