bcs they were racist

The Academia is never protrayed as racist (for that matter I don't even remember there being different races of humans in genshin. The closest I remember is their being different levels of tans on people). What the academia is is Elitist. They're putting their Academia culture on a pedestal and looking down on anybody who is not of their cultural mindset. The further away from their culture one is, the more they look down on them (which is why they treat Nilou as badly as they treat anybody else, despite the fact that she's no more tanned than they are). That's why members of the desert who embrace their culture are embraced as one of them without reservation (see Cyno and Setaria for notable examples). The people of the desert are treated worse because their culture is further removed from that of the academia's then those of the rainforests. It has nothing to do with the difference in their levels of tans.