From what I see, even good comments with facts and sources that go against the prevalent narrative are either downvoted or flagged a good chunk of the time, which discourages people from commenting(as it's meant to be) because of lack of visibility. It can also make the commenters unable to post comments for hours because HN's rate limiter kicks in, so they are effectively silenced.
Also, many times they're attacked personally and those comments violating HN's etiquette are not downvoted or flagged. Not to mention very low quality Redditesque are also not downvoted or flagged, but are upvoted, which lowers the quality of HN as a whole.