I've seen this thread for other games so I thought I make make one for X. Pretty self-explanatory topic.
First thing that comes to mind for me is Tidus. For some reason the vast majority of the Final Fantasy community hate him with a passion, yet I sincerely believe he's the best written protagonist in the series (at least out of the ones I've played); yes he whines a lot but it's not the only thing he does, he acts upbeat and cheery even when everyone else is feeling down, and always tries to keep the group moving forward through thick and thin. We finally get a character who has a broad range of emotions and character flaws, and for all intents and purposes actually feels like a real human being, yet he's even more hated than even some of the more notorious characters the franchise has to offer. Why that's so is beyond me, then again this the same community that praises Crisis Core like it's one of the better games in the franchise so maybe I'm just out of touch with the fandom hivemind or something.