In a way, iirc, it really is. It's as much a "I disagree" as it is "I don't like this". That said, I would like to see more people actually respond in addition to a downvote.
I don't think that's generally a function of the moderators though.
Nope, sometimes I would have a rebuttal but flagging is the better option (constructive discussion is hard without mutual respect, and/or don't feed the troll). Or, the comment doesn't even have anything to refute, it's just disrespectful or it's spam, or both.
I have flagged a few comments but I'm rarely mad.
And if one is mad because of a disrespectful comment, the flagging is probably appropriate too.
Or maybe you misunderstand (on purpose?). I'm saying you attribute those downvotes incorrectly. It's maybe natural to do so as an instinct -- "those people are against me!" -- but on HN it's expected to be a bit more introspective. It's incorrect to say that "people downvote because I'm right" or "people downvote because they have nothing to say".
I don't think that's generally a function of the moderators though.