Aside from the expertise represented in the HN crowd, I think another key factor is the self-reinforcing culture Y Combinator managed to build here. The guidelines aren't just some random document, they actually describe the spirit of the place - and the community strongly enforces them. This means that uncivil or contentles comments are unusually rare, which drastically improves the quality of the discussion.

Of course, the system isn't perfect (and regularly leads to the semi-justified claim that outlying opinions aren't welcome here), but on the whole it works very well.