I thought there were some interesting themes and motifs mixed in with a poorly written film with terrible characters. The faith/Christianity elements were a little on the nose, especially the part about us angering the space jockeys 2000 years ago *cough* crucifying their messenger *cough* Jesus.
The general theme with the goo seems to be that the life created echoes something about the intentions of the host via a sort of psychic imprint. Sacrificing your own life to create new life with the goo (opening scene) promotes harmonious creation while unwilling sacrifice creates life that consumes (xenomorphs). When the humans entered the pod room and the atmosphere "changed", the goo was attuning itself the to life in the room (humans), who as flawed creations driven by self-preservation will go on to spawn malicious life with the goo. The dichotomy between willing sacrifice for the sake of new life versus destroying life to preserve your own seems to be a major theme. The scene with Elizabeth desperately trying to remove her alien represents the antithesis of the opening scene, violent rejection of new life contrasting absolutely with the idea of a willing sacrifice. The two murals in the pod room represent this dichotomy clearly, with the serene looking jockey with his chest open contrasting with the xenomorph style engraving.
But humanity is shown to be capable of willing sacrifice in the film, with the ships crew and Holloway both indicating that perhaps humanity is worthy of redemption after all.
My understand of the jockeys process is that they would send a member to a planet who would sacrifice themselves to let their own DNA merge with the planet's existing life.
For whatever reason they chose to nurture and guide humanity (their creation), hence the drawings, but when humans killed space-Jesus they decided to destroy humanity but were foiled by some mysterious calamity before they could do so.
Weyland as the "villain" was less about his atheism and more about his unwillingness to let himself die, thereby restricting his own creation (his daughter). No wonder the space jockey reacted so aggressively when the representative of the species they failed to kill 2000 years ago for their hubris shows up as an old man looking for eternal life, standing next to an android.
That's my perhaps not so coherent thoughts.