1. 'God' aka Space Jockeys created humans.
2. Then 'God' wants to destroy humans, for unmentioned reason in movie, but you can safely assume it's the same reason the 'GOD' in the bible wants to destroy humanity, as in the old testament.
3. Somehow, humans managed to prevail, our race still exists, because the 'GOD' in prometheus failed in their mission due to their own bioweapon was unleashed upon themselves.
The movie doesn't explain any further but as a spiritual individual I can see the big picture. What this movie is saying..
1. There're some factions in the 'GODs' that do not want humans to be eradicated, hence, they became rebel space jockeys.
2. They sabotaged the mission to depopulate humans, by killing their own fellow space jockeys who're hell bent on the mission.
3. These renegade group of space jockeys, are lead by none other than the one known as Enki in sumerian text, Lucifer in the bible, Dajjal in the Quran.
'Satan' is basically the saviour of humanity, the reason why we all exist today in our physical form.
The so called 'GODS' we worship in holy books are nothing more than the same space jockey camps who want to eradicate us for various reasons similar to what's explained in the holy books.
So basically, that's the subliminal programming I found out in prometheus, that could lead many to conclude subconsciously, that GOD is not good, and it is those who oppose him that saved us