Looking at this topic more broadly than solely in terms of HPMOR and it's reviews, I would argue that for many people their exposure to the concept of rationality is predominantly made up of half rationalists.
Rationality is hard. It gives us tools that allow us to update old preconceptions of the world. However in practice we will often fail in our rationality due to insufficient information or other cognitive limits while still identifying our actions as being superior due to rational principles. It is very off putting to see others claiming superiority yet still be full of flaws in reasoning due to bounded rationality. From your perspective you might clearly see a flaw in their reasoning, perhaps one you can't communicate well, even if from their perspective they have applied rationality.
This creates cognitive dissonance for accepting the idea that rationalism leads to better reasoning.
EY wrote a bit about the dangerous of being half a rationalist within the body of this post if you want to continue this train of thought.
I would argue that for many people their exposure to the concept of rationality is predominantly made up of half rationalists.
Additionally, many people who call themselves 'rationalists' are, in my experience, just using the term to justify their own ideas whatever they are and dismiss those of others as automatically 'irrational'.
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: