I've noticed flagging being used similarly, too. The argument that downvoting should be used to register disagreement falls apart when you consider that only users with enough (>= 500, I think?) karma have disagreement privileges.
I think the 500 limit is justified as a means to discourage vote-brigading. Age of the account, by itself, is not a good enough indicator, because a person might create hundreds of accounts to be used for brigading at a later date.
But, yes, both downvoting and flagging can and have been abused here, despite measures to prevent them.
Flagging is extremely effective in taking content off the front page. I understand the intention, to quickly kill spam and avoid flame war topics, but it's extremely powerful in even preventing discussion on issues and it is probably a greater contribution to groupthink than downvoting comments is. Agenda setting, controlling which topics are discussed at all, is way more powerful than controlling the range of views expressed on those topics.
I think you can "vouch" for posts and submissions now to counter the flagging. Of course, that assumes you will catch them before they fall off the front page or get auto-deleted.
I was referring to comment flagging, for which there appears to be no recourse (at least from my 140something-karma account's view). Similar problem(?), though.
