Isn't the idea to upvote useful and interesting comments? A message can be of value even if you greatly disagree with the content of it.

Also remember that the top comment position often goes to a 'contra' position with regard to the story. The reasons for this are many: the supporters have already upvoted the headline; those drawn into any comment thread are disproportionately those with some qualifying/contentious point to make; commenters in general may skew to skeptical/negative viewpoints compared to all community readers.

Relative ranking of comments are not opinion polls and should not be construed as such. 'The HN community' is rarely of one measurable mind about anything. Finally, caring much about what the net-total click-voting is on any particular item may be a sign of misplaced priorities or insecurities. What's right and what's good is not dependent on anyone's polling.