Scott previously said: "I want certification for ['Prometheus'] that allows me to make as large a box office as possible. If studios don't get their money back we don't have any movies."
If your goal is to bring it the most money, that won't be done with an R-rating. But it looks like the goal was never to make a PG-13 film, since Rothman promised not to cut a single frame out of the movie, especially not to adjust the rating. "Not one frame [of 'Prometheus'] will be cut," he recently said. "If that means it's an R rating, so be it."