Humans are meant to be the engineers' offspring. It was poorly done in the theatrical cut but apparently in deleted scenes this becomes more explicit.

I do think the Alien series in general is a condemnation of the human condition with xenomorphs being the symbol of that condition. We visit places that aren't our own and we disrupt, and eventually, dominate, the food chain.

Alien is a subversion of the human condition, in that either a) we are visiting a place we cannot possibly rule, or b) something is visiting us to conquer us much like we did to others.

The xenomorphs aren't humans, but they are a subversion of the human condition: the desire to conquer, rule, and produce offspring.