My guesses, and I have nothing to back them up but imagination, would be: The planet visited in Prometheus is a military installation developing bioweapons. The Enigineer they encounter was a soldier assigned to deploy those weapons on Earth. He's hostile because he is following his orders, and may also see us as an abomination, a failed experiment. What we see in Alien is a similar weapon designed for another destination. The scale of the Space Jockey in Alien and the Engineers in Prometheus is simply a typical Hollywood screwup.
Howdy! My real name is Jack.
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