It is actually corrosion and not rust. This is due to the door being made out of steel and the hinge is made out of aluminum. Jeep did not paint the two pieces separately, they bolted the hinge to the door and then painted it. The steel and aluminum in contact without any primer or paint between them causes this corrosion. I ended up stripping all the paint off of my hinges, then spraying them with an aluminum primer and then painted them black.
Edit: sorry I must have been sleeping when I read these posts. the rust may be from water getting in the joint and the bushing rusting like hinrichs said. I haven't had the rust on the joint like you are describing