Yeah, big difference between mystery and just not resolving your story.
ALIEN: What is the Jockey? How did it get there? Why was it carrying those eggs? Interesting questions, but totally irrelevant to the story. The film isn't about that, it's about space truckers having their brains eaten and trying to avoid that. The Jockey is fun to talk about, because at the end of the day it doesn't matter.
PROMETHEUS: What's this? What's that? Why did they make us? Why did they want to kill us? These questions literally drive the characters and the plot for the second half of the film. They're the core of the characters' journeys and the reason the story's happening. But the answer is f**k you, here's a monster on a spaceship.
To highlight how unsatisfying it is, imagine if right after Ripley discovers the Alien in the shuttle the film cuts to an Engineer climbing out of a Jockey suit, revealing their true nature. That's basically what Prometheus does.
Prometheus doesn't even have the balls to say "there is no answer", it says "tune in next time, because your answers are in another castle."