In short, the story takes place within the same universe albeit not directly connected to the events of the original. There has been some misdirection on part of the film makers to help heighten interest in the film by showing glimpses and links in common with Alien, including imagery inspired by, if not designed and built by, H.R. Giger (Source). The third trailer for Prometheus shows footage of alien spacecraft shaped like the Derelict Ship and the premise to explain the "Space Jockey" inside such ship, confirming that the film does, indeed, take place in the same fictional universe as the previous Alien films, but will focus far more on the Space Jockey race (called "gods and engineers" by Ridley Scott since the early interviews) other than on the so-called "alien creature" or "xenomorph".