see the attached image.
"1" is where the rotor is squeezed by the brake pads. this area is prone to rust over some time.
2 is the portion of the rotor that CAN have some rust problems that can be irritating.
3 is the portion that can also have rust.
if you are having issues with rust on "1", drive the car more, or keep it stored in a low humidity environment.
if you are having issues with rust on 2 or 3, remove the rotors and have them powder coated in the color of your choice. the painted portion that the brake pads ride on will wear away the paint in a short amount of time. be cautious when driving with the newly cured & coated rotors!
Most shops will tape off the portion of the rotor that the pads glide across, however they usually like to cover 1/8" to 1/4" with paint to be sure the rust doesnt return.
Even that little bit will take a few miles of driving before the painted portion has worn away to reveal metal the pads can "bite". before the pads can "bite" the rotor, the response and strength or your brakes will be equal to that of a 74 pinto; dont expect to stop if a ball bounces in front of your car, so choose your route accordingly.
hope it helps!