Going off of the graffiti in that cave, it's clear the aliens' arrival wasn't as gentle as history teaches. There was a war, a time when humans were eaten simply because they were lesser. That still happens sometimes, but now it's laughed off as caveman behavior.
Something changed how aliens fundamentally view humans.
There has to be a reason why aliens went from "these creatures are pests on our planet" to thinking they're cute and wanting to "raise" them (without considering the consent of said humans). And maybe that reason has something to do with "Mom."