That's partly true, but there's also a confounding factor that contrarian posts are more likely to break HN's guidelines [1]. For example, they're more likely to be snarky or ranty. These qualities are rightly downvoted and flagged on HN, not contrariness per se.
This comes from fundamentals, unfortunately, so it's hard to change.
The trouble is that someone posting a contrary view usually feels under pressure going in. They know that their post will land in hostile territory, anticipating that the majority won't receive their opinion (or them) well, and they're not wrong. They'll probably be met not just with disagreement, but with lazy truisms and putdowns that majorities always feel are obvious.
The more contrarian a view is, the more common the majority response is not to engage with it, but to question why anyone would ever say such a thing. Often the majority invents sinister or preposterous explanations for this. (On that, see https://news.ycombinator.com/item?id=35932851.)
Because the contrarian commenter expects to be treated this way, they typically defend themselves pre-emptively with armor like snark, name-calling, and so on, presumably to lessen the pain of being rejected. It's as if there's an implicit (or sometimes even explicit) sentence, "I know you're all going to pile on me anyway so fuck you in advance."
Downvotes and flags do end up piling on such comments, no doubt partly because majorities consider them "obviously" wrong and bad, but more because of this pre-emptive guidelines breakage. This rejection only confirms the contrarian poster's feeling that the community is against them, so we end up in a tight and vicious bind.
The flip side to that bind is that when contrarian views are expressed in this defensive-aggressive way, it gives the majority a perfect excuse to keep on feeling that its views are obviously right while others are mean and bad. The contrarian ends up discrediting their own view. When they happen to have some truth on their side (as they often do), this is bad for everyone [2].
I spend a lot of time on this from a moderation point of view because it's such a tough tradeoff. It's terrible for HN when contrarian and minority views are reflexively rejected. It's also bad when guidelines breakage doesn't get downvoted or flagged. We can't carve out an exception that says it's ok to break the rules when you feel surrounded by people who disagree with you.
This dilemma is not the contrarian/minority's fault. They're genuinely under greater pressure. It's easy to stay within the rails when all you have to say is conventional and the smug majority (aren't all majorities smug?) will upvote you. It's hard not to protect yourself with barbs when you're in a vulnerable position to begin with.
Worst is when the contrarian is coming from a minority—any kind of minority, not just the obvious kinds—who have a different background from most of the community, and so naturally have different views. The majority response in such cases can get ugly quickly. I've seen mobs hound such commenters off HN, which is one of the worst things that can happen and one of the most important to protect against. It happens by itself; no one is thinking "let's form a mob and hound that deviant". It comes from the fundamentals, as I said, of how groups (and forums) work.
From a moderation point of view we have two tools, I guess, for this. The first is to try to explain to contrarian commenters the unfortunate situation that there's a greater burden on them than there is on others, and that if they don't want their posts to be self-defeating, they need to bear that pressure while writing their comments neutrally [3]. It's not fair; it sucks; but it's how group dynamics work—we can't change it. If the majority/minority demographics were reversed, people would be doing the same in the opposite direction. I don't like to tell people that they have to do more than others through no fault of their own, so I try to make it clear that I'm on their side—not necessarily in agreeing with their view, but in feeling the position they're in.
The other moderation response is to try to recognize these dynamics when they're occurring and find ways to tilt the ship a bit back towards even. It's not ok to break the rules when expressing a minority opinion, but there are ways of explaining the rules that hopefully communicate a sense of welcome along with the explanation. Conversely, when majority commenters are breaking the rules, there are ways of responding to that which add an additional layer of reproof that is appropriate to the worseness of the phenomenon.
Unfortunately these "tools" are quite insufficient—partly because they're so costly in moderator time, energy, and feeling, and partly because the phenomenon is so large and intense. I do think, or faintly hope at least, it's possible for some of this knowledge to find its way into the culture, and that the community as a whole can shift—only a little, and slowly, but for real.
[1] https://news.ycombinator.com/newsguidelines.html
[2] https://hn.algolia.com/?dateRange=all&page=0&prefix=true&sor...
[3] https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...