Sorry to say but thats corrosion under the paint. I beleive the hinges are made of aluminum, just like the mirror brackets. The only solution is to remove the hinges, completely strip the paint off the hinges, and repaint them. Mine are doing the same thing on my rear tailgate. My mirror brackets did this also, and I removed them from the doors, sanded all the paint and corrosion off them, and coated the brackets in hurculiner. It looks ok, but if I did it again I would use a smoother bedliner coating. I've been thinking of doing the same thing with my tailgate hinges, or just replacing them and painting the new ones.
P.S. Another idea is what i did on the front grill and hood of my jeep. I got tired of rock chips on the front, so I masked off the front, scuffed the paint with a scouring pad, and coated it with stone guard spray. I got it from napa in black, and it sort of has a mild texture to it, kinda like the rhino lining bedliners. The napa part is Martin Senour Paints #4004 Stone Guard Black. Its just a rattle can spray, so its not hard to use. There is one pic in my yahoo briefcase that has a summertime pic of the front, and you can sorta see what it looks like.
'98 TJ : 4.0L - 3spd - 4.10's - 33's - HP D30 - D44 w/ OX