If there are flagged comments which are not breaking the site guidelines, I'd like links to take a look at.
The moderation intention is for comments which break the site guidelines to be flagged, regardless of which side they are or aren't on. It's not possible to reach this state perfectly, of course.
https://news.ycombinator.com/item?id=46218945
That one doesn't seem to violate the rules, and there is a lot of discussion below it.
Dude, your flag function is abused to no end, and you don't really do anything about it. One of the earliest comments I've made was one on semi-recent X11 history, and got flagged for it, because apparently everything is political now.
At least one of mine, for example: https://news.ycombinator.com/item?id=46219068
95% of flagged comments don't break guidelines in any given discussion. flagging been used forever to silence "inconvenient facts" and "dissenting opinions"
as example, just below there is reply to you saying that flagging been abused, been flagged