The film started out as a prequel to the original Alien film.
Some recent history: there had been talks of a fifth Alien movie for years, with alternating contributions from James Cameron and Ridley Scott. In fact, Scott had committed to an Alien sequel or prequel about ten years ago, but aborted the project when the studio opted to make the AvP movies first, and Scott was no supporter of the Alien/Predator crossover franchise. After the disappointing box office from Aliens vs Predator: Requiem, the studio shelved the AvP franchise again to go back to the original plan.
The prequel film was supposed to cover the origins of the Weyland-Yutani Company.
However, recently it has been announced that the film will not be an Alien film at all, but rather an original project called Prometheus. Some ideas for the aborted Alien prequel may be used, and the story may contain elements reminiscent of the Alien backstory, but it will be a movie separate from the Alien Universe. As such, the future of the Alien series is now unknown.
Though this is said not to be an Alien movie, according to Skymovies.com, there is a rumor that the Aliens and the Space Jockeys will appear in this movie and that they are building a Space Jockey set, but no confirmation has been made yet.
According to Michael Fassbender, this is actually an Alien movie, he says it takes place in the Alien universe.
http://moviesblog.mtv.com/2011/02/11/prometheus-alien-michael-fassbender/
Until more details emerge, it is hard know for certain. It currently seems that Prometheus is a film which takes place in the Alien Universe, but is not directly connected with the main storyline of the original Alien films.