The Engineers are planet builders who seed planets with the gift of life. It's shown in the start of the film that the Engineers visit Earth repeatedly, as their figure pointing to a constellation of stars is found throughout history.
When the film starts, an Engineer drinks the dark fluid, that starts this chain reaction of life. This fluid is so powerful, that it can turn a dead planet into a living Earth.
When the crew of the Prometheus lands on the alien planet, and they enter the tomb their foot steps uncover worms that are preserved in the tomb. They are still alive and crawling. The tomb cylinders start to leak the black fluid and the worms mix with the fluid. These worms evolve into the snake like creatures that later attack the two crew members stuck in the tomb.
Later, only the Prometheus captain refers to the black cylinders as bombs or weapons. When Elizabeth is talking to David she asks why the Engineers would want to destroy Earth, David replies "sometimes before you can create you must destroy".
I don't think the Engineers were going to destroy Earth as much as "restart" it. It's clear they took an active role in making our planet, but they had some kind of agenda that isn't defined in the film.
This is why, at the end of the film Elizabeth flies to their home world. To find out why the Engineers had decided Earth was a failure.
I answered this question two years ago, but since then a lot has been revealed about the plot for Prometheus by Ridley Scott. The following comes from various sources that I've read.
At the start of the film. Illustrations of figures pointing to the stars implies this was a message from the Engineers. Ridley stated in an interview that there is nothing in the film that indicates these figures were Engineers, and the pointing could have been a warning not an invitation.
Ridley says the early planet shown at the start where an Engineer sacrifices himself was not Earth, nor does it indicate if it was a historic reference or present day.
Ridley Scott has said in an interview that the reason the Engineers wanted to destroy Earth (specifically mankind) was because Jesus Christ was an Engineer. The Engineers made man, man went bad so they sent an Engineer to try and fix the problem. We crucified the Engineer and apparently they didn't like this.
There are many other controversial topics related to the film, but I decided to only reference the things that came directly from Ridley.