Spectacular digital effects, of which there are plenty in Prometheus, are complicated, time-consuming and expensive. Likewise, impressive sets and cinematic hardware cost money. Orchestral scores and booming sound design aren’t cheap either. Had Ridley Scott dropped the ball in these departments, it might at least have been understandable, given the number of people to be coordinated and the sums of money involved. But the script, on which everything else in a film has to hang, is one of the cheapest parts to get right. It typically involves a handful of people, not hundreds of technicians racing against the clock. Not getting the basic story and dialogue presentable, or even close to presentable, is much harder to excuse.
And yes, this applies to any number of other films.
Update: The particulars of its badness can be found in the comments. Spoilers, obviously.