I think the reason people still make the connection is that there are still too many bigoted people who think that other races are as "alien" as that, unfortunately. I don't think it's to do with the context of the story so much as the problems that exist in our societies (I haven't played it yet, so this is just a totally stabbing theory, but one that always interests me).

If everyone alive had an accepting and rational attitude about race relations, cultural identity and cosmopolitanism, as the once you are voicing here, then I think it wouldn't be a comparison we make when analysing Sci-fi (but perhaps so much of the stuff wouldn't focus on relationships with aliens then eithe), but I don't know if we will ever get there, xenophobia is just... ingrained in a lot of people. And people will always project their own observations about society onto fictional characters, even if it doesn't always hold true (I'm not calling pluto a bigot for seeing it either, I know why she sees it: I recently quit a job I hated because everyone else in the office didn't understand how racist they were and it hurts to be constantly exposed to people who are ignorant and complete unable to realise how ridiculous they are, still genuinely do think that foreigners are subhuman).