Here’s the thing I have a hard time accepting in Logan- the other X-men are gone. The movie never explicitly says what happened to them, but the strong implication is that they’re dead (and in general the position is that most mutants are dead). If they’re not dead they ALL abandoned Charles (apart from Logan).
But, really?? They’re ALL dead? None of them are still around to help out Charles and Logan when they desperately need it? That scientist dude, who couldn’t take down Logan who’s not healing and a bunch of kids, some how managed to kill ALL the other X-men?? Storm, Cyclops, Jean, Colossus, Iceman, Shadowcat, Nightcrawler, Mystique, Angel, Rogue, Gambit… ALL of them were taken down??? That’s a big claim.
I think the implication was that Xavier killed them, inadvertently, during one of his episodes. It was established in prior movies that if Xavier concentrates too hard while connecting with another mind, it has fatal consequences. The effect we see whenever Xavier loses control in Logan is identical to that which occured during the climax of X2. That’s why Logan and Caliban are keeping him in total isolation while sorting out his titration.
It doesn’t have to be all of them dead, though. (I think the specifically say “several?”) Just the ones in Salem at the time.