I think it's partially a matter of what it lends itself to naturally, and as a baseline being able to manipulate or detect thoughts is pretty dystopian if you don't go out of your way to do something else.
It's also narratively difficult to make the POV characters capable of reading thoughts and still have any interesting mystery, intrigue or conflict. I'm reminded actually of Star Wars, which goes out of its way to make sure every single important character is immune so the story doesn't fall apart.
Basically it's just way easier to make a genuine psychic evil, because if they're capable of doing almost anything along those lines it's really hard to make them the good side and not also make a completely boring story. Stellaris doesn't have that problem, but its also a lore made of 90% references so it inherits the result.
That's the case when they're extremely powerful and there are no passive barriers to psychic powers (no mental walls, no way to resist a psychic or detect subtle influences). But the same is true of pretty much anyone with absolute power of any kind (fictional or not): absolute power corrupts absolutely.
Lots of franchises have restrictions like "nothing but surface thoughts can be read without great concentration and very obvious intrusion", "actually influencing someone's mind without being noticed (so they can e.g. retaliate if not restrained) requires extreme subtlety and misdirection, like secretly manipulating someone for weeks under the guise of nightmares", "minimal training or even just strong willpower can give someone mental resistance, possibly ironclad against anything but brute force", "minds are resilient and bounce back to their natural state fairly quickly, unless the influence is reinforced for months", etc.
The result is that villains can use mind magic to directly coerce people they could have coerced anyway (legions of troops that feel no fear replacing forced conscripts, mind controlled heroes after being abducted/tortured), incapacitate (or briefly dominate) people, etc. and good/neutral characters can use it for things like determining if someone is telling the truth (or demonstrate their own truthfulness), ulta-mega-therapy, communicating ideas/memories or sharing senses, far/future sight, etc.
Ex. James Cameron's Avatar effectively has psionics... it just requires that you literally plug one mind into another through the nerve-tentacle-thingy, so it's hard to use unless consensual (except when taming animals). And it's not even remotely evil, or at least not portrayed that way.
Or Valdemar series (YA fantasy novels, by Mercedes Lackey), where 90% of the mind magic is done by the good guys, and it actually manages to not be secretly sinister, because (essentially) everywhere that mind magic training is available also has anti-mind magic training (and actual domination is apparently only possible with the addition of conventional magic and physical torture).
I think it's only easier to make the psychics evil if the psychics are absurdly powerful compared to the average person. Because it's really hard to not make someone with absolute power vaguely villainous, in general.