A post will die on it's own if it fails to receive upvotes. If you think something else should be on the front page, you go and upvote something else or leave a comment on the article explaining why it is crappy (comments down-weight an article). If you can't find something else that's better, then move on and stop acting like some gate keeper of worthy content.
If everyone behaved like what you're suggesting, the front page would just be a bland pile of the lowest common denominator content that displeased the fewest number of people.
This is all beside the point that flagging is (no matter what it ought to be) an extra signal that has broader uses than merely spam/rule violating. I could also argue that "off topic", a use mentioned earlier and on the guidelines, is sufficiently broad and subjective that "something I think the HN community would be better off not discussing" fits "off topic". In any case the flagging mechanism is still there. The site does remove flagging privileges if you use it too often, so there is clearly a sense of how flags ought not to be used too often (or else you lose them) but that hardly influences why flags ought to be used.