Part of the problem is that news aggregates reward people who comment early, and the earliest comments are the kneejerk reactions where you braindump thoughts you've had brewing but don't have anywhere to put. (Probably without actually clicking through.)
Still, I believe what makes HN unusually nice is just the stellar moderation. It is definitely imperfect, but it creates a nice atmosphere that I think ultimately does encourage people to try to be civil, even though places like these definitely have a tendency to bring out the worst in people. Having a deft touch with moderation is very hard nowadays, especially with increasingly difficult demands put against moderators and absolutely every single possible subject matter turning into a miniature culture war (how in the hell do you turn the discussion of gas ranges vs electric ranges into a culture war?!) and the unmoderated hellscapes of the Internet wrongly painting all lightweight moderation with a black mark.
I definitely fear for the future of communities like HN, because the pressure from increasingly vile malicious actors as well as the counter-active pressure from others to moderate harder, stronger, faster will eventually break the sustainability of this sort of community. When I first joined HN, a lot of communities on the Internet felt like this. Now, I know of very few.