It's because church have been a dark organization coated in light pretty much for all it's history, so of course most story would show them that way. Many pope in the past did unforgivable things, most obvious one is of course the witch hunt, which happened because the pope was paranoid. Also while the church aren't as evil nowadays, they are still far from being a light organization they like to make others believe.
It’s like the Rising of the Shield Hero pope all over again
Not just fantasy. Even in bible, the one who join hands and actively sought Jesus prosecution is none other than the so called High Priests. They were so damn convinced that they were right and commit all sort in wrongdoings while proclaiming that they were God's man.
uh... yeah...
Some of RW religions do have that, especially on the dark age... even if it wasn't on the scale of religion yet, some cults of some faiths were darker than it seems to be
I really would like to see a proper church with a non-evil pope for once. It's one thing that in rl the church had some problems, but it's a different matter entirely that every goddamn manga/webtoon/novel/whathaveyou paints western religion as evil. They wouldn't do that to their own - oh no, their good gods are always good and their priests are always holy, but the moment it's based on the western religion? Childeating, murderous, satanic fanatics. Fucking hell. I've a big tolerance, after the first few times I've seen this I stopped giving any fucks, but over the years the sheer number of works demonising western religion started getting to me recently.
the pope of all people? seriously?...
sigh... i guess every church/religion in a fantasy world has a PRETTY dark side...