2. What's Wrong With Us?
So assuming the crew of the Prometheus are correct and their DNA checks and theories are right... we come from The Engineers. So if we accept that and cross that over with the opening scene of the film we can conclude they made all life on Earth. Throw the ancient artworks into the mix and there's a history of interaction too. Whether it's one, or even multiple Engineers over a long period of Earth history is up for debate but it seems the 'experiment' with humans led us on a path to build structures like Pyramids and civilizations for thousands of years and then for some reason or another The Engineers had a change of heart. Judging by the carbon dating Shaw took from the decapitated Engineer in the ship (let's call it the Juggernaut) 2000 plus years ago, The Engineers were about to embark on either wiping out the human race or changing it (more on that later). Given Promethues is set in 2089 - 2094, it's a safe bet that what the writers and Ridley Scott are implying is that the birth of Christ or even the birth of religion is what caused The Engineers to get snippy about their creations. False Gods and wars about faith are legitimate reasons to go to war given actual human history, so spreading the net further to include our actual creators "The Enginners' taking offence to this makes sense to me.