I don't think it's rationality per se, but rather flamboyant displays of exceptional intelligence. For most people, this is very difficult to like.
Given the social dynamics involved, I suspect this isn't easily fixable.
There's a difference between displays of intelligence and excessive displays of intelligence. A working definition could be that it's excessive when its purpose is to show off rather than to communicate the point at hand. (I think we agree here, just sort of thinking out loud and making sure.)
So obviously it's a bad idea to show off. To me the question really is what do you do when you need to communicate something, but doing so will be seen as excessive. What are the best strategies to mitigate the perceived excessiveness?
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: