I'd agree with that. Comments I disagree with that are well-thought-out often add a lot to a discussion, or at least to my understanding of what's going on and other people's points of view.
I do tend to downvote comments that contain obvious factually-incorrect information, though, even if the information seems to have been provided in good faith.
How often do you upvote comments like that? Those comments you disagree with, yet are well-thought-out, add a lot to the discussion or at least your understanding of what's going on and other people's points of view.
I don't think people do that enough and it leads to comment-bloat. "I'll make my point and then add in a platitude to draw in the upvotes, hopefully balancing out the downvotes I'll get for my opinion."
I'm probably slightly biased toward upvoting comments that I agree with, assuming similar good quality, but I tend to upvote comments I disagree with fairly often as well.
I do tend to downvote comments that contain obvious factually-incorrect information, though, even if the information seems to have been provided in good faith.