Because quite simply, 'the fans' are not a single person - whereas Xhaka is. Again, you are right in a vacuum, but this is football and I do agree he was justified to be frustrated and tell the fans to fuck off. But looking bigger picture here, you can't punish 'a fanbase' - even if you're talking about 0.01% who is actually doing this sort of thing. Sure, you can start removing fans from the ground for booing people, but then you start banning users online who abuse them, why not remove comments who are negative too? At the end of the day reacting against the fans rarely goes well for a player, even if it's the right choice in the moment to say 'I don't deserve this moment'.
In many ways it is a lot like tailgating the person who cuts you up and sticking your fingers up for them to see in the mirror. Sure, they're in the wrong - your actions are justified, right? But you're still acting the idiot.
I was okay with Xhaka, as I felt his reaction was justified. But your explanation gives me pause. Xhaka didn't deserve this, but I agree now that he probably shouldn't have reacted in the way that he did. However, I don't agree with this part:
But looking bigger picture here, you can't punish 'a fanbase' - even if you're talking about 0.01% who is actually doing this sort of thing.
You absolutely should be taking some steps with your fanbase, not punishment necessarily but something. The way your fans have gone about with the team is not going to attract any decent players. The decent ones currently present may even want to leave.
IMO, the first thing that should happen is to get rid of AFTV. Spreads toxicity in the fanbase, and makes mountains out of the smallest molehills.