This is only for a subset of comments, but one common case that's sometimes sort of accidental: a commenter disagrees with a submitted article strongly, but doesn't realize that the article is written by the submitter or by another HN user. If they had, they probably would've phrased their disagreement differently.
Of course it's nice to be polite when disagreeing with any article, but I notice myself making more of an effort to be polite when disagreeing with an HN user's own submission, compared to disagreeing with, say, a New York Times article, because the NYT reporter isn't present or going to read my comment. HN's greater volume of user-written content (compared to, say, reddit) makes this something not everyone expects to encounter; it's like ranting about how Daikatana sucks and then realizing that John Romero was standing right next to you, and then you feel bad.
(This doesn't explain mean-spirited comments that are responding to other comments, though.)