Interestingly this has been flagged, but there's only a couple of replies that I can see that are grey, and only a couple that's critical of the article and sub

Interestingly this has been flagged, but there's only a couple of replies that I can see that are grey, and only a couple that's critical of the article and subject. But I can't see any flames at all, just the usual HN courtesy. Is the auto flag mechanism to do with up and down votes of comments? Does that make some comments controversial? I like upvoting comments that go against the stream, but would that mean that the whole discussion gets more likely to be auto flagged? Would a user's best bet be to go with the crowd (and to downvote or not vote up such dissenting opinions) ?