this. the thing is when i was in the fandom several years ago, there was plenty of drama and discourse -- the prevailing attitudes from certain popular bloggers at the time about mulder's depression in the revival (ie that it was funny and deserved and that scully shouldn't go back) was what made me step away back then -- but mulder being an atheist and a non-christian was a non issue. most people doing mulder meta and writing fic etc actually liked and admired him for being brave enough to believe what he'd seen and felt and not in the sets of beliefs and disbeliefs that are socially popular.
But now there's a huge amount of pressure from what feels like a loud majority of the fandom to engage with the idea that the only morally correct way to like mulder and be an 'appologist' for him is to either believe that he's Secretly Christian Underneath and is just too traumatized to admit it, or that you have to constantly condemn his atheism and non-christianity. Also there's this weird layer of like, because CC got all hooked into his Scully-Madonna complex in the later mytharc, and because Scully had her (dubious and alarming) "religous episodes" as some of her main solo themes, many people see it as basically misogynist of mulder to not believe in the christian god.
Meanwhile the man is textually Jewish coded, confirmed Jewish in the marginalia and played by a Jew-by-Descent (who seems to have his own complicated beliefs and spirituality, but i mean the whole born into the tribe but assimilated thing does put you in a confusing place) and textually believes in some level of theism or animism, just not the christian god specifically. His beliefs aren't actually inconsistent, they're guided by his experieces while leaving the door open to spirituality. What he has a problem with is universal, proselytizing religions (as opposed to ethno-cultural religions) and grift that takes advantage of vulnerable people. mulder also turned on the UFO people, denouncing them as grifters and marks when he thought the whole thing was a hoax, which again, consistent belief system. But it's like almost no one is willing to listen past him refusing chistianity to understand what he's saying, it's just "mulder is mean, mulder is closed minded, mulder is sexist and insensitive to godly [woman] feelings.' I've even seen some posts about how mulder would be more likable if he'd "hear her out" about catholicism, and way too many fics where once they're together, there's a scene where, to paraphrase, scully's like "come to church with me" and mulder's like "oh i can't go in there with my blasephemous nature but you go pray for me i probably need it," as if it's a forgone conclusion that she's Right about christianity and once they have sex he will Of Course acknowledge that even though he's still stubborn and Unworthy... No, actually! Mulder is already morally and spiritually complete as a Non Christian. Non christians don't need to convert or "admit" that "the bible" or christians "might have a point" or "might be the real truth" (that was another post i saw, that One Breath/scully was telling mulder via scully's headstone -- that she didn't need! -- was telling mulder that the real Truth he'd been searching for was Faith [in the christian god]) to be a good person or to be fulfilled or to like them without requiring disclaimers.
And you're right that the obsession gets into the mytharc too, which is frustrating and fuels the rest of it. It's disappointing, too, because i do actually find the mytharc interesting and parts of it are really involving, and contrary to popular belief it did make a *kind* of sense that worked by a fairly consistent science fantasy logic. But then CC got obsessed with this mystical christianity tangent, and it didn't lead anywhere feasible on television so he had to back out of it, and then there was just. well, the less said about season 9 the better lol. And i even readily admit that the scifi gnostic christlike mulder spiritual battle for earth thing would have been an interesting story if he'd had the time and technology and the endgame in mind to go for it, and if the show hadn't been long established as more "normal" scifi paranormal horror... like, it would make a good novel series. In the context of the existing tv show however, not so much. And then it just feeds into the popular fanon idea that mulder is just stupid and backwards and wrong about everything :/