Yeah the one founded by an open wizard supremacist who created a snake monster to kill children he considered to be impure. The one named after him hundreds of years after his death.

Snape feels like this stand-in for authority Rowling does not like/ does not want the reader to like, or a cheap plot device to trick readers into accepting Harry's lack of development. Two things that come to mind:
Philospher's Stone: After Harry stopped Voldemort from getting the stone he is asking Dumbledore in the infirmary what happened after losing consciousness. Harry asks about the red herrings and Snape's demeanor that suggest Snape was the true culprit. Instead of something reasonable like "Snape protected you because he is a teacher, it's his job and there's a huge difference between being nasty to discourage bad behaviour and wanting to harm you" Dumbledore says that Snape resents Harry's father and that he helped Harry because he owes something to his father or something like that. Harry thus walks away without having to reexamine his own behaviour.
Prisoner of Azkaban: When Harry sneaked out when he was not allowed to Snape catches Harry and starts interrogating him. The scene felt like we were supposed to see Snape as obstructive and not Harry as being irresponsible for sneaking out to places where he should not be when there is a (alleged) killer that wants him dead on the lose.
Note that these were all in the first few books, way before the incel stuff got introduced.