It all depends on what part of the rotor is rusting. Can you post a pic of the rust?
You can't put anything on the braking surface of the rotors as that would interfere with braking.
All you can do is to replace the rotor with one that uses a stainless steel braking surface.
If it is the bobbins that are rusting, once again, buy rotors with stainless steel bobbins.