I'm wondering if the big alien simply assumed the humans were just another form of xenomorph and thus just attacked them by reflex.
Maybe the space jockey had already been infected and the xenomorph had been gestating for a long time. And now that the space jockey was dying it burst out of him to save itself.
We have seen infected people in frenzied states in other Alien films, so maybe that was part of what was driving the space jockey's violence toward the humans?
I think it's more simple. Before things went pear-shaped for the Space Jockey's, they were preparing a mission to wipe out life on Earth (my guess as a test for their bio-weapon). So they have no love for us to begin with. Then when we wake up their last survivor, the first thing he hears is an android telling him, "Oh hi, we're here so you can save the life of my boss over there".
It would piss me off too.