I'm with Guillermo del Toro - this film really owed H.P. Lovecraft a story credit for At the Mountains of Madness. The black goo is analogous to the Shoggoths. It's a tool created by the Engineers to genetically modify whatever it touches, like the worms. It can create life (as in the first scene, which I took to be the origins of life on Earth), or be used as a a bio-weapon to destroy it. But also like At the Mountains of Madness, it became too powerful to control and eventually killed its creators... The details of which are ripe to be explained in a sequel.