HN is smaller. When you have a forum of this size the members will be much closer to the ideals of the site (i.e. if it's about civil discourse then everyone will respect that, if it's about being a troll that's what you'll get). As the sites get larger you start getting closer to the average amount of kooks/idiots/assholes/etc. I can't think of a single site that got big and didn't have this.

Facebook is an interesting take on this by effectively blocking you from hearing much from people you don't wish to hear from.