They do represent an aspect of the community. Not the community as a whole - you seem to assume that every criticism of a part of the community is an attack on the whole - rather a toxicity within it that seems to be growing, albeit slowly and not without resistance. That it is growing isn't a reflection on the users and moderators as much as the society that feeds into the community. We can only do what we can, but no one can command the tides.
To pretend this toxicity and bad behavior is something alien and wholly detached from the community, or that because comments are flagged and killed they don't represent the community, is specious and counterproductive. All of it is the community, good and bad. This rising toxicity and anger and cynicism is a real problem, and if you didn't take every criticism of the community so defensively as you seem to, I think you'd agree.
No, I don't know what can be done about it, but I'm certain it's not a problem that can be solve with software classifiers. I'm not going to be ashamed for pointing it out and complaining about it, either. If we simply quietly downvote and flag but otherwise stay silent, then there's no social pressure against that kind of behavior.
But I know you don't like repetition so I'll try not to do it that often.
People already do speak up.
I just don't think that HN has a general homophobia problem. Such comments are definitively outliers and are dealt with by the mods and the community. The only thing I would complain about is that it doesn't happen fast enough for a site like this where posts come and go quickly.
https://news.ycombinator.com/newsguidelines.html