I almost hate to discuss this because these are things people should figured out on their own, but this is a thread to discuss this. All of these clues were right there throughout the film. Consider all of the facts shown in the film, and consider each is there for a reason.
Milllennia ago we were created by the Engineers when they seeded the Earth with the building blocks of life, or if you prefer, they were sent here to create us by their creator. In this act, an Engineer sacrifices himself to create this life. They use a black substance they either created, or was given to them by their creator.
The Engineers wanted us to find them one day, hence the images they left pointing to the location of LV233's star scattered throughout history for us to find, all pre-dating the rise of the Roman Empire. Some of these images indicate people may have worshipped the large beings who point to the star configuration.
The five buildings on LV233 with the heads carved on the tops were clearly temples, meant for worship. The main chamber in was a sanctuary, with a giant Engineer head as the focal point, painted mural on the ceiling depicting an engineer with his arm around what looks like a biomechanoid creation, et cetera. There is also a sculpted mural depicting a biomechanoid being resembling the xenomorph we all know very well as a focal point in the temple. The temple is full of canisters of the black DNA altering substance. The intention was that humans were to come here one day, to worship the Engineers as Gods. The substance in the canisters was intended activate in their presence and and to change them into something else.
The Engineer ship in the hangar in front of the temple is full of these stacked containers, in various sizes. Call it a weapon now if you like, since that is now what they are. The Engineers brought these in those ships from somewhere.
2000 years ago mankind was at the height of civilization, and we were doing some very awful things in the Roman Empire, including the killing of ******. ****** was the one man who was trying to get us off the path we were on.
At this same time, the Engineers decided to take the black DNA altering substance back to Earth and destroy mankind (or were being sent to do so, if you like), or looking at it another way, to remake it. The black substance accidentally, or intentionally, infected the Engineers in the temple, killing most. Regardless of whether or not the Engineers created this substance, or were given it by their creator, they could not harness or control it. One of the Engineers made it to the pilot room and sealed himself in one of the suspended animation capsules to avoid infection. Over the years the temples were eroded and worn down, in disrepair, indicating no Engineers have returned LV233 since the incident.
Over 2000 years later, the Engineers creations finally arrive at the temple, lead by Shaw and Holloway, intent on meeting their maker. David discovers that the Engineer ship was going to return to Earth with the containers. The containers in the temple room are activated by their presence and start to release their contents. The worm like organisms on the floor are altered, or an new organism grown inside them, creating the ass-flower snakes. They in turn impregnate the humans with another organism.
The holographic images showing the Engineers running through the hallways 2000 years prior seem to indicate one engineer was running from the others, to the temple room. This one could have sabotaged the black substance allowing it to infect the others, they could all be running from the contagions to the ship for escape. They could all be running from something else, but there is nothing to indicate this. Regardless, they were clearly infected in different ways, some dying from the organisms growing in them (piled in the hallway), some infected with the virus that changes them into something else (the virus in the Engineers head that caused it to explode). A member of the crew (the Captain as I recall) proposes that these temples were really some kind of a military installation holding weapons of mass destruction.
I wont get into Weyland's, or any of the individual characters motives, as they are very clearly defined in the film, and they cover the range of imperfect human behavior and motives, as well as the better qualities indicated by the sacrifices several of the characters make to save the others. Their individual fates are also tied to the action each character takes. Note that each person who is infected by the black substance is also altered in a different way, related to their character.
When the Engineer in the ship is awakened he sees this group of humans, his own kind's creation, before him. He then finds the one who speaks to him in his own language is not one of his creations, but an artificial being made by his creation. He destroys it and kills the man responsible for its creation, then attmepts to destroy the rest, as he was going to do anyway by going to Earth. He is clearly disgusted with them, what they have done, and what they have become.
Creation vs creator themes are scattered about the film. The Engineers created life, or were given the tools to create life (the black substance). Their creation turned out to be flawed in their eyes, so they decided to destroy it. Weyland is directly responsible for creating a new life with his self aware replicant-androids. David, who clearly resents his creators, has flaws in his character directly related to the flaws in them (ala Roy Batty and Tyrell). Shaw is barren and cannot create life, but the black substance causes the Cthulu-facehugger thing to be created in her, which then turns on the Engineer responsible for her creation. This in turn causes a new being to be created from him in his destruction, the only other one shown in the temple mural. We already know what the purpose of that being is. The Xenomprph exists only to destroy ALL of these creations.
Note Shaw is a woman of some faith, specifically, Christianity. It is important to note that they arrive on LV-233 on Christmas day, and everything ends on New years day. Shaw asks the question about the Engineers near the end of the film that anyone would ask - "who created them?". It is also interesting to note that David put Shaw's father's cross in a jar on the Prometheus, but at some point he took it out and kept it with him. The fact that she took her cross back implies that she clearly still believes that there is the possibility of a creator (her sign-off voice over is "...last survivor of the Prometheus, in "the year of our lord" 2094, still searching), does not necessarily think it was the Engineers, and she wants to know why they changed their minds and decided to kill us. That answer should be obvious to her, but she still wants to know all of the answers, which leads us to the next chapter...
I loved this movie.