After reviewing a number of after movie discusssions, reviews, blogging, etc. and then seeing the film for myself, it would seem that things that I thought were obvious and heavy-handed when it came to the explanations were not when it comes to the majority of the public. With that in mind, I have created this explanation for hopefully the majority of the questions posed in and about this film.
PLEASE NOTE: This explanation containes MAJOR SPOILERS for this film and possibly following films for anyone not having seen PROMETHEUS. To begin, I will add some "cannon" that may help preface some of the setup for the films. Please know that while the following films (even of the AvP variety) were not necessarily well done, they ALL conform to this cannon and are consistent in this fashion:
1) The Alien from the original that spawned the sequels is commonly refered to as a xenomorph. The reason for this is that it is supposed to be the ultimate in bioweapons as a species annihilator as it is able to adapt to whatever host it impregnates.
2) That is why it has varient looks throughout the sequels. In Alien 3 it takes on the characteristics of a dog as it burst from said animal. In the AvP universe, it is why it took on the Predator characteristics with its impregnation. Alien Ressurection showed a film where humanity was able to catch up to the genetics of the xenomorph enough to perform a certain amount of modifications themselves. Again, please bear in mind that while I don't think that these were nearly crafted so well as the first two films, they DO adhere to this maxim of the series.
3) With the xenomorph now known to be a bioweapon for the Space Jockies (Engineers is what they were called in PROMETHEUS), we can now view the first six films in the series as what happens when we stumble across just a tool of the weapon masters.
In PROMETHEUS, we get to meet the ultimately more terrifying creatures that are the weapons designers themselves. If they created the xenomorph, what else can they make? If they are like people in this sense, they are surely forever looking to create more effective and terrifying weapons all the time. What horrors have they evolved since that time?
Again, please know that once you read the following, you CANNOT unread it... hence, they are MAJOR SPOILERS. This is your last chance before having the major reveals of this and following films shown to you.
The easiest way to go about this is to explore the motivations for everyone involved both as characters in this film and creator of the story. I will first begin with Ridley Scott for the over-arching scope of this film.
EVERYTHING that was shown in PROMETHEUS was shown for a reason. Some films are shot. Some are put together. Others are crafted. Having seen the film, I firmly believe PROMETHEUS to fall into the latter. It starts with the name PROMETHEUS and the story it invokes. They explain it in the film, but I will rehash it for the purpose of this read:
In Greek mythology, Prometheus gave fire to mankind at his own peril and to his ultimate penance. He was charged with the creation of the form of man, while Athena gave man life. In creating man, Prometheus came to love his creation more than the Gods that "employed" him (presumably since the Olympians had defeated and banished his titan bretheren). His interactions with the Gods led Zeus to take fire away from man. Prometheus' response was to promptly give it back to them. It was for this defiance that Prometheus was then punished by being chained to a rock where an eagle was to tear out his live for all of eternity.
There are other nods within the story about Pandora and Prometheus eventual release that may play into later movies' allegories, but the preceding paragraph gives us our start. It provides the framework of understanding the nature of creator and creation. The entire film dons this theme throughout its framework. Engineer creators and people creations. People creators and android creations. Engineer creators and xenomorph creations. God as creator and Engineers as creations. Weyland as creator and his daughter as creation. The allegory provides a severely layered look at the structure of this entire film.
How much does a creator have disdain for his creations when they act of their own accord rather than to their makers' will? If Prometheus serves as the allegory, then not all makers will regard their creations equally. Which brings us to the motivations of the first character of the story... the engineer at the beginning of the movie.
The presumption on my part is that the planet that we first see in this film is Earth in its primordial stage of development. The Engineer that we see is what I believe is our first Prometheus. Literally, he drinks the elixer to begin using his own body as the beginnings of life on Earth that would eventually lead to the birth of modern day man. His stripping of his clothes is a common archetypal image of shedding the confines of old thinking to birth himself anew. This was possibly a shedding of the warnings of his fellow Engineers to not do what he was about to do. Hence, it would explain the motivation for the existence of people as being abominations to many Engineers in spite of what one of their own had sought to begin in the first place.
The second character in this chronology is Weyland. His motivations became clear in the third act of the film and actually drives much of the plot in PROMETHEUS. As a man with presumptively tremendous clout and power, he is faced with the bane of all power-hungry men: death. "No one gets out of live alive" is how the saying goes. Weyland, in the waning days of his life has put all of his effort into finding a way of circumventing this maxim.
With this as the backdrop for the true purpose of PROMETHEUS's mission, Weyland becomes the most evil character in the film. His existence provides the motivations for David and Vickers as the story of PROMETHEUS unfolds. When Dr. Shaw comes to him with information regarding remarkable evidence of aliens seeding life and then providing the map to meet them, he is presented with his hail mary attempt at cheating death. This could even be tied to the first of the AvP films where Weyland draws from his own ancestry to support evidence of significant extraterrestrial life. If this were integrated into his back-story, he could very well draw on this as motivation to not dismiss Shaw as an out-of-hand maverick with doe-eyed aspirations of meeting her own maker.
From here, we can more easily draw the motivations of the major protagonists of the film and why things unfold as they do. Vickers is born of a love loss between emotinally unavailable father to his daughter. Shaw is born of unyielding faith against all that is seen in favor of what is unseen. Other people on the mission serve as pawns in Weyland's motivation with respect to finding the beings that could spare him death and then serving as guinea pigs for ad hoc experiements with severely advanced bio-technology and David serving as the one to execute the procedure and then report the results.
David is actually what becomes the character that is actually central to the entire film (and maybe the entire series). Of everyone reveled, his character is the one whose motivations are kept secret from us. We are given hints at his inner workings, but we are never fully given to his realization of whether his actions are born of "childlike curiosity" as purported by some or as severely calculating to make him the new driver of the film and its subsequent stories.
While most would dismiss David's actions of hastily opening doors "just to see what would happen", I would submit that he is more like a triple agent. He dons the mask of making a show of being a butler to the crew's whims while doubling as the scientists' understudy/research compiler, a protege of sorts for Weyland himself knowing full well that he is little more than a means to an end for an evil man, and a personal agenda that can span the range of all sorts of ideas. This range could run the gamut from being a personal vendetta against all of mankind to becoming a Prometheus himself by becoming the chooser of who lives and dies in the stage that he sets throughout this film.
I believe this is why Ridley chose the cast as he did for this film. He needed the major players in this film to be heavyweights in the acting realm to pull off his execution of this story. I believe that his casting of Idris Elba as the ship's captain was the icing on the cake to actually put some real glue to his narrative for what would otherwise serve as loose ends in his epic.
This will end my first run of explanations. I will get to my second run when I am less tired. In the next couple of days, I will finish the rest of my explanation and respond to questions that you may pose as they come up.