The real reason is that Alien overall was a far better movie and thus worth closing a blind eye to its own logical fallacies.
Right, so all these discussions of Prometheus' lore and whatnot are moot. Setting all that aside, it was a totally forgettable movie. I didn't scream for my money back when it was over, but I didn't (and still don't) have any desire to watch it again.
And to those who would argue, "well you're in here discussing it so obviously it made an impression," well, I wouldn't be discussing it if it weren't brought up, and I'll be the first to say I had very high hopes going into the theater.
Steam + PSN: PHJF