Weird. My experience has been the exact opposite. Rarely do I get downvoted for comments merely because people disagree with it. It happens, but often enough for it to be a problem. IMHO, the benefits from seeing unconstructive comments downvoted has been more beneficial than the damage done from the occasional good comment that gets downvoted because someone disagrees.
At the end of the day, a good comment will always get more upvotes based on its perceived quality than downvotes from people mis-using the downvote feature. I credit this to the fact that you only get downvoting privileges at 500 points, at which point, you've been around long enough to have a sense of the HN culture. At 500 points, you feel like you're receiving a great power that comes with great responsibility.