Wouldn't say there is much hate towards HL, I'd say people have their preferred game-mode and choose to play either in one or the other or both. Anyone who truly thinks 6v6 players perceive HL as a threat is extremely paranoid and over-protective of their preferred gamemode, anyone who actually is a 6v6 player and thinks HL is a threat is extremely close minded and unaware of what is happening in this game on a player-by-player level. Hundreds of people who started in HL moved to 6v6 for a variety of reasons you can only fathom to do with the weaknesses of the HL gamemode.
Both gamemodes have positives and negatives, for sixes a lot of the TF2 playerbase won't like it simply because there isn't a Pyro and Pyro is their favourite class - Not a weakness in the eyes of many a 6v6 player, but to a person who invests their time in that class, why would they want to play a gamemode where they can't/shouldn't play it 98% of the time? That is the big advantage of Highlander, it opens up competitive TF2 for everybody that plays the game, whether you're favourite class is Pyro, Heavy, Spy, Engineer, Sniper or the classic 6v6 classes, either way you have a competitive gamemode designed for you to come in and learn more about your class and play. Isn't that the point of competitive TF2? Anyone who wants to turn this into an "us vs them" scenerio is an idiot and is damaging the scene, sadly people do it but the hate towards Highlander is only really towards the gamemode itself opposed to the community (bad attitudes exist in both formats), I can fully appreciate why people would hate playing 9v9, but what 6v6 players don't appreciate it people have their reasons for hating 6v6 gamemode as well and they are the opposite values that 9v9 incorporates. (unlocks, class limits, class selection, map choices..etc).
Big problem with Highlander is there aren't enough people who contribute it and remain proud of their gamemode to put down coverage regularly in the form of articles, interviews, and just visiting forums and expanding the community. People who take it seriously are extremely closed off from the wider spectrum of the competitive community therefore people can only base their judgements off of what they read, watch and limited experiences of 9v9.
TL:DR - Both competitive formats are great in their own ways, both scenes should work together to be part of a "wider" competitive TF2 scene because a player playing competitive TF2 is better than a player playing public TF2.