That's because Ridley set it up as an intended trilogy - and you don't give all the answers in part 1 of a trilogy.
But if a trilogy (or even a sequel) didn't happen, Ridley also wanted to frame things in such a way that the answers were right in front of you - you just had to bring your brain into the theater with you and "read between the lines."
OK, Borgified, to sum up what we've all been speculating/analyzing:
The guy at the beginning, one of the Engineers, was on prehistoric Earth circa the beginning of the Cambrian Era (650 million years ago). His self-poisoning was a religious/terraforming ritual [The upcoming Director's Cut will make this more explicit] intended to jump-start the evolution of the primitive one-celled life already present on Earth, via a combination of the mutagenic black goo and the Engineer's DNA. Hence the planet is "seeded" with a variety of complex plant and animal life. One of those forms of life, after nearly all of that 650 million years (and at least two asteroid-caused "reset buttons"), assumes a sentient form almost (but not quite) identical to the Engineers. Noting this, the Engineers visit Earth repeatedly beginning in the Stone Age, setting themselves up as the "gods" Man will come to worship and spurring the development of human civilization (presumably along the lines of their own). The first of these civilizations, the Sumerian Empire, is the closest to the Engineers' own (including written/spoken language). Recurrent throughout their lessons to early man is what only their modern-day descendants would recognize as a starchart leading to the Engineers' home star system.
Somewhere around the 1st century AD, the Engineers (for reasons as yet known only to themselves) change their minds about Man and decide to hit the reset button on Earth a third time. A ship is readied to take off from the Engineers' scientific/military outpost on LV-223 with a bioweapon cargo intended to eradicate Man and (presumably) steer what life is left on Earth in a direction more to the Engineers' liking. ("Sometimes to create, one must first destroy.") Yet the weapon they create, using a variant of the same black goo mutagen used ages ago and the DNA of a different alien lifeform (the green "amber" in the temple's central chamber), proves too deadly for even the Engineers to handle. All but one in the outpost are killed, the sole survivor already in cryosleep when the outbreak happened and thus was spared. Following this disaster, the Engineers briefly resume their God identities on Earth, starting over with the primitive natives of Central and South America, before finally washing their hands of us somewhere around 700 AD.
While it's not made explicit in Prometheus
, we're clearly supposed to believe what we know as the Xenomorph "Alien" was the product of a different-but-similiar bioweapon experiment of the Engineers intended for another of their seeded worlds, one that apparently predated the LV-223 project by some considerable time and, again, proved too much for the Engineer in the ship that crashed on LV-426 to handle. What we see happen to Holloway/Shaw/the Engineer in the film is what presumably would have happened on 1st century Earth to the whole human race had that ship made it with its cargo. And, like it or not, that's as close to an Alien
prequel/setup as we're probably going to get. The main questions the two sequels now aim to answer are: Why did the Engineers decide to destroy us way back when? Do they still
intend to destroy us? Were we crafted for some specific purpose, or did they make us "just because we could"? Were we a mistake?