If you (or anyone) run across a flagged comment that isn't tediously repeating ideological battle tropes, pushing discussion flameward, or otherwise breaking the site guidelines, you're welcome to bring it to our attention. So far, the flagged comments I've seen in this thread seem correctly flagged. But we don't see everything.
On this site, we're trying for discussion in which people don't just bash each other with pre-existing talking points (and unprocessed rage). Such comments quickly flood the thread on a divisive topic like this one, so flagging them is essential to having HN operate as intended. To the extent possible at least.
(oh and btw, though it ought to go without saying, this has to do with the type of comment, not the view it's expressing. People should be able to make their substantive points thoughtfully, without getting flagged.)