While I was reading the thread, this comment just posted mentioned that the site founder, pg, has endorsed the idea that the site's rules permit downvoting to express disagreement. By the site rules, implicitly, some comments should be downvoted on sight.
http://ycombinator.com/newswelcome.html
"Essentially there are two rules here: don't post or upvote crap links, and don't be rude or dumb in comment threads."
Yes, downvote thoughtfully, and downvote to improve the overall quality of discussion here, but a downvote in an active discussion to silently indicate a comment is 1) uncivil and unconstructive, or 2) factually incorrect, or 3) both is okay.
A comment that is solely on the issue of being downvoted is subject to being downvoted on sight, because those sorts of comments are never constructive to the discussion and disfavored by the site guidelines.
http://ycombinator.com/newsguidelines.html
"Resist complaining about being downmodded. It never does any good, and it makes boring reading."
The site founder, pg, (who no longer has an active day-by-day role in moderating the site) has commented that downvotes for disagreement are permitted here.
(In order of time of posting.)
"I think it's ok to use the up and down arrows to express agreement. Obviously the uparrows aren't only for applauding politeness, so it seems reasonable that the downarrows aren't only for booing rudeness."
https://news.ycombinator.com/item?id=117171
"IIRC we first had this conversation about a month after launch. Downvotes have always been used to express disagreement."
http://news.ycombinator.com/item?id=658691
"I sometimes downvote things that seem mistaken. I think most users do."
https://news.ycombinator.com/item?id=1006808
"If there's one thing I wish I could do to improve HN, it would be to detect this sort of middlebrow dismissal algorithmically.
. . . .
"The problem with the middlebrow dismissal is that it's a magnet for upvotes. The 'U R a fag's get downvoted and end up at the bottom of the page where they cause little trouble. But this sort of comment rises to the top. Things have now gotten to the stage where I flinch slightly as I click on the 'comments' link, bracing myself for the dismissive comment I know will be waiting for me at the top of the page."
https://news.ycombinator.com/item?id=4693920
This is an ongoing issue, but the key idea is both to upvote and to downvote (and, for that matter, to submit stories and to post comments) in way that elevates the quality of discussion here. Grow a thick enough skin to learn from other users' behavior here, and develop curiosity about why other users might disagree with you, and all will be well.