The only issue I have with powder coating is the fact it tends to flake in areas such as the drilled, relief holes in rotors. I had drilled rotors on my 03 Cobra for a short while, but they kept cracking. I tried powder coating them, but the coating kept "popping out" of the drilled holes and on some of the cooling fins.
Mike's method works better and costs mucho less bucks. You can pull the wheel and liberally spray paint the rotor edges, the cooling core and the holes; forget the paint you get on the braking surface. Your first good "stop" will remove all evidence of your artwork.
Whenever you lose a little paint in the holes, just spray the tip of a Q-tip with your black paint and swab the bare areas.