For the longest time I was confused at seeing down-voted comments because I mentally assumed that downvotes mean "this is a troll comment / this is some kind of abusive comment". Not so.
Also (and I've said this before so apologies for repeating myself!), if downvotes do mean 'disagreement', could we get rid of the graying out of down-voted comments, or maybe just make it an account preference? I'm interested in reading viewpoints that I might not agree with and graying out the comment makes it really hard to do so. It also seems to fit better with the model of "downvote = this comment shouldn't be in the conversation".