Aren't we all forgetting something big and obvious[1] that's staring us in the face? :-/ There are people out there for whom "rationality" is counter to their values! Imagine someone who reads the horoscope every morning, who always trusts their gut feelings and emotions, who's a sincere believer in homeopathy, etc etc (whatever you think an irrational person believes). Such a person would probably strongly rationality, rationalists, and the complex of ideas surrounding rationality, for probably understandable reasons (i.e. if a group consistently belittles your treasured beliefs, you're liable to hate and dislike the group). Such people might dislike R!Harry because they'd see rationality as a magic feather, and seeing it working in the story (to an uncanny degree, I might add) would be reading an author tract for them. Imagine a black person reading a fanfic where, through the power of !RACISM! (exaggeration mine), Harry gets everything handed to him on a silver platter.

[1]disclaimer: just because it's big and obvious doesn't mean it's actually more right or important, but only that it's easier to see and think about