Prometheus was a sci-fi movie with little action, following 20 years of underperforming Alien sequels and spin-offs. Doing over 400 million worldwide was anything but a failure. Not to mention that Ridley's involvement rescued the franchise from DTV hell after the atrocious, cheap AVP-R.
At that point, however, not calling it "Alien", and claiming that it sets up a whole new universe, was the smart thing to do.