Besides upvotes, downvotes, and flags, there are software penalties like the flamewar detector and various anti-abuse measures, and moderation downweights. We do a lot of the latter—I don't want to underemphasize this. The HN system is a combination of these three subsystems.
You're right that user flags do more than mods do, just because the numbers work that way: there are many orders of magnitude more users flagging things than there are mods.
Edit: 5 orders of magnitude more, in fact!