The only thing that Prometheus really puts humanity at the center of galactic events is the idea that the Engineers were explicitly en route back to Earth to come directly after us because of something we did in the past - which is a plot point that I could really take or leave and would have been more than ok if the film had dropped that angle to push us a little bit more out of the Engineers' direct focus. I also would have been happy to toss aside Prometheus' "100% DNA Match" angle.
The Engineers making humans on Earth, and seeding (and, perhaps, later destroying?) a multitude of other worlds and populations in the very same way (remember, Ridley never directly confirmed if the planet in Prometheus' prologue was Earth because, at the end of the day, it doesn't matter whether that one is explicitly Earth or not. That's what happened on Earth... and on other worlds as well.) ultimately serves to make humanity even less significant in the grand scheme of things. Earth is nothing more than Petri dish for one of the Engineers' many scattered experiments, and a failed one at that. They made us, as David said, because they could - and they made others for the very same (lack of) reason. We don't have some grand purpose. Earth is a discarded world that held on longer than it should have, full of beings that don't matter. And even our greatest creation supersedes us and, using the raw materials taken from the Engineers, creates something 'perfect' that functions as a sort of plague in the known universe moving forward.
I should also add, none of this really even seeps into my mind when watching Alien anyways. It's pretty easy for me to watch each installment and take it as it as it is with what's presented directly on screen, under the conditions it was made in, without constantly needing to cross reference each "canon" material in my mind. When I'm watching Alien, the crew finds a mysterious ancient craft full of eggs. David, the Engineers, etc. don't really factor into my mind, until I'm off watching the prequels and taking in their particular spin on the material. When I'm watching Aliens, the third act isn't made any less exciting knowing that Alien 3 kills off Hicks and Newt as the opening credits roll.
