SO

In the the intro scene, one of the Engineers is seen drinking some of the black ooze, and then seemingly disintegrate at a molecular level. His DNA is seen to break up and then reconstruct again, as if to hint that this particular individual's sacrifice allowed genetic material to be spread on earth and allow the spontaneous forming of new life forms (us), which is why the Engineers' DNA is so similar to ours.
The individual in question is apparently left alone on a barren land (Earth ?) as if abandoned there, maybe cast away for a crime he committed. We would then be seen by other Engineers as the soiled offspring of a dangerous criminal, come to seek our revenge.

This one individual from the intro, one of the Engineers, having given us the greatest gift of all (life) by betraying his own kind, would then be comparable to the mythological Prometheus. Alternatively, he could have been left there to start with for betraying his kind by granting us a gift that allowed us to rebel against his kind : Prometheus again.

Flash forward several thousand years, the Humans reach that remote moon, and find thousands of jars of the black stuff, loaded in a ship with navigational data to Earth in its central computer... Two explanations for that : 1-The Engineers did create us, but we outlasted our planned purpose and they were planning to come and de-compose us to serve as base for a new experiment. 2-We did rebel thanks to the guy at the beginning or we did originate from his suicide and represent an abomination to the Engineers, and they were coming to clean up the mess. That would explain the surviving Engineer's reaction when confronted to live humans...

Now, the Aliens... The black ooze by itself doesn't seem to spawn Aliens, but it does appear to affect DNA and cause fast mutations, and worms can be seen crawling on the floor of the "cave". My take is those worms mutated when they became exposed to the black ooze (DNA decomposed and recombined) and attacked the Engineers. The new mutated worms retained their initial parasitic method of reproduction, but their mutation have enabled them to combine their DNA with that of the larvae's hosts, hence why we don't see an Alien looking even remotely like the Xenomorph until one incubates and hatches from the last Engineer.

That's my take on things...

Now two things I couldn't quite explain :

- Why would the pictogram left on Earth point to such a barren place of no real relevance to us except it looks like a staging area for a fleet tasked with destroying us.

- What is David's deal with the black ooze, and why infect Holloway ? I didn't quite get the "Great things have small beginnings" part. What was he trying to achieve by infecting the doc, and how did it fit in Weyland's plans ?