I wouldn't have said anything if you concluded "you're not nice" from the first part. But you conclude it because they don't like when someone messes up traffic? That's wrong.
The complaint isn't about a friendly wave. The complaint is that it's someone's turn to go, and instead of going they wave at someone else to insist the other person go out of turn.
The wave is an insistence of "you go first", not a greeting or a thanks.
I'm not, and after checking the website of multiple driving schools in my country, I guess this is a fairly deep cultural difference - they all mention that you can always let the other driver go first by courtesy, and that adaptation to the situation overrides the base ruleset.
The issue is that very often it would only take you a couple seconds to go through anyway, so you end up forcing the other person to adapt in a way that leaves everyone either the same or delayed.
There are definitely places where letting someone go is appropriate, especially if it's leaving a gap so they can make a turn. But if you're on a road and you have to wave them through then most of the time you're not actually helping, and fake-helping is an annoying thing.