I suppose if you really can't stand the main character, there's not much point in reading the thing.
I was somewhat aggravated by the first few chapters, in particular the conversation between Harry and McGonagall about the medical kit. Was that one where you had your aggravated reaction?
I found myself sympathizing with both sides, and wishing Harry would just shut up--and then catching myself and thinking "but he's completely right. And how can he back down on this when lives are potentially at stake, just to make her feel better?"
Yes, I did find that section grating. I'm describing my emotions post-hoc here (which is not generally reliable), but what I found irritating about the first few chapters was the fact that Harry acts in an extremely arrogant way, nearly to the point of coercing the adult characters, and the story-universe appears to back him up at every turn. This is the "Atlas Shrugged" effect described downthread by CellBioGuy. Harry is probably right in most of those arguments, but he is only so effortlessly correct and competent because the story-universe is ...
I was reading reviews of HPMOR on Goodreads and I noticed that the people who didn't like the book were essentially "put off by the rationality". They thought Harry was arrogant and condescending.
Then I was thinking, a lot of people are "put off by rationality" for similar reasons. What a shame. There's a lot of value in spreading rationality, and this seems to be a big obstacle in doing so.
Any thoughts on how to make people less "put off by rationality"? I think the core issues are: