It's a longstanding tradition in SF/fantasy racism allegories to have characters who are bigoted against aliens or robots or fantasy creatures, but are fine with other human races, and often who are themselves nonwhite (e.g. the real Hank Henshaw in this very show, or Will Smith's character in Bright). The whole point of allegory is that it isn't a one-to-one, literal match to the thing it symbolizes.
Besides, it's a fact of life that prejudice is often selective and inconsistent. There are plenty of people who have nothing against other races but are homophobic, or who would welcome a female president but not a Muslim one, or whatever. Prejudices are overcome one at a time, not all at once. So it's perfectly believable that someone could be fine with other humans but still hate aliens. If anything, the existence of aliens would make people more likely to perceive a common identity with other humans.