You can go overboard in inventing a scenario and details for this, but going strictly by what is presented in the film, there is a somewhat clear cut layout of who the Engineers are and why they did what they did. Lets just go strictly by what is presented in the film.
Ages ago the Engineers seeded the Earth with the building blocks of life by breaking down their own DNA, creating the building blocks for complex life. Life developed from this, including mankind, who share the same DNA as the Engineers.
The Engineers visited Earth many times, and humans illustrated them pointing to group of stars in the sky, over and over throughout history. By the dates of these artifacts in the film, we know they visited Earth within the time frame of 35020 BCE to 680 CE. Maybe earlier, maybe later.
Many of these images indicate humans worshipped the Engineers gods, and the Engineers most likely posed themselves as those beings. The things they were capable of probably appeared god-like. They likely were responsible for the origin all early deities that mankind worshipped, including Sumerian, Egyptian, Babylonian, Greek, and Mayan gods. This is implied in the art the film makers chose to use as the artifacts.
Humans later discover these ancient pieces of art all have the same star configuration and surmise that it may be an invitation to meet our makers. In 2073 they discover where this configuration of stars is located in space, and determine the Engineers are likely from a moon, LV-223, orbiting a planet around one of these stars. Neither the premise they put forth that this is an "invitation", and the probable location they have chosen due to it being Earth like, may be accurate.
The Prometheus arrives at LV-223 in 2093. The five dome shaped buildings discovered on LV-233 with skulls carved on the tops appear to contain temples, meant for worship. The main chamber appears to be a sanctuary, with a giant Engineer head as the focal point, painted mural on the ceiling depicting an Engineer with his arm around a biomechanoid creature (that we have not seen before). The exact meanings are not clarified in the film.
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 entire life cylce of the alien we know from Alien is also depicted. There is an altar with a bowl on top in front of the altar. The exact meaning of this is not clarified in the film, but one would assume this was an altar meant for worship.
The large head in the sanctuary room may be that of the Engineer's creator, NOT an Engineer. The head sculpture includes rib-like features not found in the Engineers features, along with writing on the cheeks. It also may very well be a head of the Engineer, just stylized. The ceiling mural may imply the biomechanoid creature is a creation of the Engineers, or this may be the Engineer's creator that is illustrated, hand around another of its creations. The temple is full of ampules of a black DNA altering substance. Overall, the intention appears that this room was meant as a place of worship. The exact meanings are not clarified in the film.
The skulls on top of the domes perhaps the domes actually served another purpose, and this image was used to warn others that this was a dangerous place. The substance in the ampules appears was intended to activate in the worshipper's presence, but to what end? It is all very alien, and not clarified in the film.
The Engineer ships in the hangars in front of the domes are full of these stacked ampules, in various sizes. From a human perspective these are weapons (as the Prometheus crew surmises in the film), and the ships that contain them are ships of death. There are multiple hangars around the temples, indicating a whole fleet of these carrier ships are present.
The ampules were possibly manufactured in another section of these domes. The domes may simply be factories for the mass production of this substance, and the ship hangers are there for loading this cargo for transport. This place may be nothing more than a weapons depot, and the crew of the Prometheus comes to this conclusion in the film.
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 ******, then later ****** was worshipped as the Son of God and the Savior of mankind. The Engineers visited Earth both before and after this event.
For some reason, around 2000 years ago, the Engineers decided to take the black DNA altering substance back to Earth and destroy (or remake) mankind. In the process, the black substance was accidentally, or was intentionally released, infected the Engineers in the temple, killing most. Over the following 2000 years the temples were eroded and worn down, in disrepair, indicating that no Engineers have returned LV233 since the incident. This makes sense if the whole area was considered a biohazard after the outbreak and abandoned.
The 2000 year old Engineer in the ship is awakened. He sees this group of humans before him, a creation of his own kind. He then finds the one who speaks to him in one of the ancient earth languages is not one of his creations, but an artificial being made by his creations. He destroys it and, knowingly or unknowingly, kills the man responsible for its creation, then attempts to destroy the other humans.
He is clearly disgusted or angered with them about something, and powers up the ship to go to Earth and complete the Engineers mission to destroy mankind, according to David. The question still remains, why do they want to now destroy what they created?
This is where you have to examine the Christian symbolism presented in the film. There is too much of it to ignore, and no, it does not mean ***** was one of them. It does not mean other religions may not have contributed to the cause either, but Christianity is the only one presented in the film.
Symbolism - The Prometheus arrives on LV-233 two days before Christmas, Shaw's creature is removed from her abdomen on Christmas Day, and she leaves LV-223 on New Years Day. This totals seven days. The captain playing "Come all ye faithfull" on the squeezbox, Shaw's cross, the story elements of faith presented in the film, and several others.
The Christian references are there to clue you in to ****** as a catalyst for the Engineers decision to destroy (or remake) mankind. Seeing as how the Engineers are more into using rather hellish methods of creation as we see in the black substances, they do not seem to be the benevolent or kind beings in any way that humanity would recognize, very much the opposite of anything ****** like.
Considering that they continued to visit the Earth upwards of 600 years after ******'s death, long enough to witness ****** being declared the savior of mankind and the worship of him as the son of God, this seems the more likely reason they were en route to destroy mankind, or possibly start over. The Engineers created man, and man worshipped them as gods. Mankind had now stopped worshipping the Engineers as Gods in favor of another.
There can be other theories, but this is the only reason I can find presented by the evidence in the film for the Engineers to want to destroy mankind 2000 years ago.