The long shot of the tunnel entrance to the facility shows it is in the face of a tall mountain. The closer shot shows that the mountain is only a little taller than the doors themselves.
Granted the Hulk is worth studying when captured, but at this point in the series he would not be mistaken for an alien. Everyday people have encountered the Hulk as well as having received nationwide coverage from Jack Magee, so surely an advanced establishment like Prometheus would have heard of him.