Ok, so in abstract stuff and gameplay stuff, I'll go gameplay first:
Gameplay: your runners infilitrate Humanis. And they find the relatively dull workings of a minority political party. There is no super secret source of funding; there's campaign donations, some from corps, some large private investors, a bunch of twenty yen donations from people who get a stylized "i'm with Humanis" button back. Because, in the sixth world, these guys aren't any more whacko than a Sanders supporter. Their elaborate super secret plan for Seattle? Continue to influence the city council and mayor, maybe even hold some seats, and promote/support Pro-Human legislation. Don't give your players some super rewarding target to hit, because there isn't one. There's maybe some lobbyists, some PR kids, some town hall meetings that your middle school teacher goes to when shes feeling politically active.
Remember, these guys helped put Brackhaven in office - they are large enough to be normal. They don't need to burn a cross on your yard; they have a zoning committee for that, and I guarantee there are 50 good reasons for that zoning change beyond "I don't like orcs." If you really want to put the boot in, have your players work hard to dump the paydata on something, expecting ti to be a public outcry - and then have all the talking heads and politicans from both sides of the aisle agree on open trid that this is actually a pretty solid plan, and might really do some good. There is not really much of a reason to have super secret night of rage 2076 plans when you can do it all in the open.
Have some of your contacts uneasy about dealing with your runners after so many anti-Humanis runs. You are, after all, effective attacking a mainstream political party. "Hey men, yeah, I sell you guns and you murder people for biz, and that's ok because thems the rules of the game.But there's a line between "runner" and "terrorist" that maybe isn't so clear and word on the street is you might be on the wrong side of it. I pay the right bribes to the right people, and runners quietly go fuck up some corp drek in a private war, no one cares. Same corp probably sends a team to me for guns going the other way. Hell, same team might run aginst that corp tomorrow. My name starts getting associated with "terrorists" who keep attacking policlubs because of its "moral?" All of a sudden biz isn't so good and I fall into the liability column. So yeah, you're gonna have to cool off a bit before I deal with you."
Heavens help you if your runners use violence. One trid of a snarling trog sammy gunning down humans - licensed private security contractors in a very dangerous world! - or an elven mage using magic, and you just recruited more members to the Policlub than you ever could have hoped to cut out through your run. And, incidentally, totally justified all those "private security contractors" they keep around. Can't you see that there are misguided meta racists out there who will resort to violence because of an opposing political view? These are definitely NOT brownshirts, they're needed security!.
If they do find some link between Humanis and Jackboots for Jesus? Turn those tolerance cannons around. How dare they assume that a few Violent Extremists, bad apples really, represent the entirety of a legitimate political movement. You bigots. That should be the "educated society" response to most smear efforts. The appropriate uneducated, of course, will happily agree that humanis are shitheads. That's why their in Sons of Sauron! We can only handle the humans through violence, am I right?
Lets see..other good events to pull...have your players cause a race riot by being too violent and the story of seven dead humans, killed by trogs (facts optional) for NO REASON! (again, facts irrelevant) gets out. Leave a couple dozen dead, a few hundred injured, and a barren;s community last public school burned down. In the ensuring racial tension, everything the players are working for is set back several steps and humanis comes out as a force for moderation, which then boosts their poll ratings.
Abstract Stuff: On the abstract, fear is just as often based on competition for scare opportunity/resources, conflicting ideology, etc.The fear was/is still there. Understanding is a way to avoid conflict, but there are several significant and fundamental reasons why you can hate and fear even that which is understood. Positional and interest differences, fundamentally non-compatible ideologies, who determines the norms and values you live by, so forth and so on. We mostly view these as "State" issues and not "people" issues - people issues we say are just a product of misunderstanding because those big things are taken care of by states. The relationship of interests, resources, and values has, for most of the western world in recent history, been a state one.
In a sixth world where the state is on its way out, those fundamental fears are very rapidly becoming people issues, "us"/Them" issues. Next thing you know, murdering the shit out of your Tutsi neighbor because he's non-christian and therefore can't be trusted - indeed, is probably planning to enslave you and your hutu friends - and you know, incidentally, may be sitting on some pretty good grazing land, starts to make a lot of sense.