While this is true, there can be a distinction between a character with flaws and a character who is extremely irritating to read about. And this is one of those judgement calls where The Audience is Always Right; it seems very reasonable to stop reading a story if the protagonist noticeably irritates you.
In general, commentary to the effect of "you should like this thing" is not very useful, especially if you are trying to figure out why someone reacted negatively.
(These discussions in which one group has an overwhelmingly strong "squick" or "ew" reaction and another group does not are fascinating to me, not least of all because they seem to pop up quite frequently here, e.g. about Eliezer's OKCupid profile and NYC cuddle piles. Both sides spew huge amounts of ink explaining their emotional reactions, and yet there never seems to be any actual sharing of understanding. In the interests of trying harder...I was also very aggravated by the first few chapters of HPMOR, and would be happy to discuss it calmly here.)
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?"
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: