I'd add: (1) the community doesn't necessarily agree about what's legitimate. I don't see any evidence that the flags on this one are less in good faith than the upvotes; (2) upvotes can't be the only factor determining HN's front page; that would make it consist of controversy, gossip, and fashion, and undermine the reason why readers come here in the first place.
There are also other mechanisms, such as vote-ring-detection, that can kill a topic as well.
(That is my current understanding anyway, I am not HN staff, and I am not saying whether I agree/disagree with any of these mechanisms, just stating them to help alleviate your confusion about why some topics may be doing very well and then suddenly die -- it's not always because of flagging)
I've heard about this before and it still sounds crazy to me. I comment quite a bit, and almost never upvote topics. Using the standard "other people are like me" heuristic, I deduce that the normal operation of HN involves automatically killing all the topics.
It's more likely that other people are in fact nothing like me, but I'd like to understand this a bit better.
That seems like an awfully low expectation of the average HN reader IQ.