IF they are done right.
The most common problem I see is that a group can not be fanatically for being fanatics. Nor can it be fanatically for being a nuisance to the main characters. That includes being fanatically against some group. "Being against" is not a view. There will be some reason for their views, and if the reasons are false, you have to give some human reason why. (If you think that this is not realistic, it is one of many things where things in fiction need more justification than those in real life.) It gets silly when the antagonist is depicted as hostile to some particularly angelic group -- and particularly silly when you get things like prejudice against vampires being treated as obviously wrong despite their habit of drinking people's blood. I have read with my own eyes a story in which a woman lets off a ghoul that's committed repeated murders with a warning and then rages against a man who killed an unintelligent monster that preys on human beings on the grounds that he should have watched and seen whether it was dangerous. (Indeed, the story tempted me with a story idea about a fanatical organization that preserves all monsters as the man's tries to exterminate them, and the rebel character, like the woman's ancestor who split with this group, is one that wants to kill when the unintelligent ones are dangerous, or the intelligent ones murderers.)