As it was mentioned above, most of my hate for it stems from people recommending it around the Internet as the pinnacle of HP fanfiction. I've seen this mostly on reddit. Some random Harry Potter TIL post? There it is in the comments, "oh man you should read HPMoR it's so good/rational/right/fixes the canon". Fuck you. There's literally millions of HP fanfics and this is the best one? Fuck you.
I have a feeling (substantiated by nothing) that a lot of people who are really into it are the kind of people who post in /r/atheism and other rationality/atheism obsessed parts of the Internet.

As for the story itself, I tried to get into it a few times over the years, mostly when I wanted to read new fanfics and there was a dearth of new material, but was never able to get past the first few chapters. It just wasn't interesting to me in any way.

The first fanfic I remember reading was on mugglenet's forums. I really, really enjoyed it at the time, and I have fond memories of reading it, but I'm not going to pretend it's not shit now, because it is, and it was then too. I just didn't know better at the time, and hey, it got me into fanfiction.