A recent New York Times article talked about Ridley Scott’s desire to tell a spiritual story in Prometheus:
On the phone from London, where the film was mostly shot, Mr. Scott described it as “ ‘2001’ on steroids.” He said he liked Stanley Kubrick’s notion of “a police agency in the universe that will give a ball of dirt a kick.”
“God doesn’t hate us,” Mr. Scott added ominously. “But God could be disappointed in us — like children.”
...and this latest featurette does not shy away from that.