Down-votes and up-votes are just two sides of the same coin. There is nothing inherently wrong with one versus the other. It's unfortunate that the down-vote is labeled with a flag in the UI though because that gives the wrong impression as to its use.
It does help to report a spamming user to someone with great voting power: a high-value down-vote will reduce the reputation score of the spammer, and hopefully ultimately discourage them from posting because they will get little or no monetary gains from it.
I think you are right.. the flag does send the wrong message entirely.. good call there.. the flag makes you feel as if you are only supposed to hit if for porn, or egregious offenses. It just needs to be a simple thumb up or down.. to encourage more liberal use for articles that suck.. similiar to Youtube, FB etc.. Everyone will get more downs I'm sure but that is the nature of the beast and would encourage you to provide solid content and engage your users one on one..