I think HN is better than many other websites, but certainly worse than some. Obvious reasons:
1. Internet disinhibition effect enhanced by pseudonymity - anyone can create an account called 'internettoughguy3' and start talking shit to people; blatant sockpuppetry/nastiness is punished by the mods, but one can get away with it on an occasional basis.
2. Common interest in hacking-type stuff brings together people whose views diverge on other things, like religion and especially politics; conflict ensues.
3. Persistence; sort of the opposite of #1, many of us have been here for years and know how to 'push each others' buttons,' so lingering dislike or disagreement between individuals will occasionally boil over into a cutting remark.
4. Geeks tend to be introverted and so less good at social modeling. http://xkcd.com/610/ sums this up, though I think the dig at Ayn Rand fans is a bit unfair because such thinking is equally prevalent on the left.
None of the above apply to me, of course. I am perfect.