Traditionally the karma points were supposed to indicate what you felt contributed to the discussion, then I think it was pg who said that using them to indicate agreement was also okay. So now there's essentially a second point system, for indicating what does and doesn't belong in the conversation, but they are much more serious.
I guess I can see people flagging posts that are relatively unconstructive more liberally now, things that would maybe just be ignored before. Maybe that's a good thing, I don't know.