I think some behaviors which may be considered arrogant can be justified. For example, dismissing other people's opinions out of hand can be a good choice when actually surrounded by people with very low-quality opinions.

As for appearing arrogant to others - it may be a difficult-to-avoid side effect, or it may have value of its own - there are social contexts where acting arrogant is useful.

Is it arrogant for HPJEV to consider himself to know better than the adults around him? Maybe so, but he's right about a lot of these things. (I believe there's a significant subset of HPMOR would-be readers who found Harry insufferably arrogant. Does that mean he should change his behavior?)

Having tabooed "arrogance", one of the interpretations is "emotional attachment to the idea of one being right". That, I think is a real problem for an aspiring rationalist - you need to be able to consider the possibility of being wrong.

As DanielLC says, you should calibrate yourself and neither strive to underestimate nor overestimate your abilities.

I want to be able to assure myself that this or that intolerable academic will be magically punished with a decreased capacity to do good work

(If they aren't well-calibrated, that seems like a likely outcome.) Edit: not sure about this part.

I think a lot of what folks call "arrogance" is just a basic failure to be instrumentally rational in interpersonal communication.

Probably for most people, the unwillingness to assent to the opinions of the higher status, the authorities, or the majority is intellectual "arrogance".

How dare you think that you can know better than The Bosses, The Authorities, The Masses?

I'm increasingly of the opinion that truth as correspondence to reality is a minority orientation.

You might say that they are both traps, at least from a truth seeker's perspective. The arrogant will not question their belief sufficiently; the humble will not sufficiently believe.

By "arrogance" do you mean overestimating your abilities, or just being annoying about it? The first one is problematic, but so is underestimating. You should calibrate yourself and get an accurate view of your abilities. The second one seems to be more about some kind of signalling. It has an obvious disadvantage of alienating people, but it must have some kind of advantage or people wouldn't do it.

I forget who said this originally, but much of rationalism is internalizing the fact that you, yes you, are prone to all manner of biases and mental tics that lead to error. If 'arrogance' as it's being used here is something that interferes with recognizing the errors that you're making in any given moment, then arrogance is certainly antithetical to rationalism.

On the other hand, I'm fairly used to people thinking of me as arrogant in person-to-person communication, and when they give me that label it never has much to do with my willingness to admit error. Usually it has to do with my vocabulary, or other patterns of behavior that they interpret as a desire to be seen as intellectually superior. If that's what 'arrogance' means, then it's more orthogonal to rationalism. Heck, arrogance as an affect might even be rational in certain circumstances, depending on how you want to be seen during particular social situations.

If you are actually concerned quite a lot with being better than other people, and your challenges are not directly competitive or collaborative in nature (if you're trying to invent something in your garage, or write well, or do well in classes that aren't graded on a curve), then that form of arrogance is probably a failure mode. It implies that you're performing a social role, not trying to succeed, and so you'll tend to optimize for best appearances and not best results.

Discussing "humility" and "arrogance" is difficult without careful definitions. I was thinking about this recently; this is how I would like to define them.

Whenever I end up feeling like I have been arrogant, it is because I underestimated someone else's abilities, and I ended up surprised by what they were capable of. If humility is the opposite of arrogance, then humility is the ability to accept, as your prior, that somebody you meet just might end up being more wise or more accomplished than you. To be arrogant is to fail to realize that you might have something to learn from other people.

(These definitions of arrogance and humility thus only relate to mental habits, not to social behaviors.)

Note how this makes humility valuable -- if you expect everyone around you to be dumb and inferior and not worth learning from, if you don't give others the chance to prove you otherwise, you're going to miss out on everything that you could be learning from them. I wouldn't expect your putative arrogant academic to have very many fruitful collaborations.

So yes, I would say that arrogance is bad intellectual hygiene -- it's having the wrong priors about the people around you.

Note also that it's also possible to be unfair to oneself in this way. Impostor syndrome should not be confused for humility. High self-esteem should not be confused for arrogance.

... I realize only after writing all of this that there's also intellectual arrogance and intellectual humility; it seems that they can be modeled the same way, but with ideas instead of people.

I believe you're confusing arrogance and closedmindedness. There is a correlation between openmindedness and intelligence. I do believe openmindedness is a form of rationality. I'm not sure how good rationality training is at increasing it. Personality Psychology indicates Openness to Experience is a fairly stable trait; not one that can be taught.