There have always been mean/dumb comments on HN, but in the past they were routinely downvoted to -4 and then ignored. The problem is that now, people have begun upvoting them, and there are more upvoters than downvoters. Thus, the reason this is a problem is a change in voting patterns, due to a shift in community makeup and expectations.
Partial solution: when a mean/dumb comment is killed by flags or moderators, send an automated warning to anyone who upvoted it and apply a token karma penalty. Increase in severity for repeat offenders -- from a larger karma penalty to no longer counting their votes to a hellban. This educates those who simply don't understand that mean/dumb comments don't belong here, and removes those who continue to intentionally violate guidelines.