Simplest way to get rid of brake rotor rust (if it truly bothers you) is to do a few hard 60-0 braking tests in a safe area. Rust has to be grinded off. It's cheapest to let your brake pads do it.
If you really want to be anal, you can use compressed air to blow off water droplets off the rotors after you wash your car to slow done rust generation. Personally I'd rather just do a few hard braking runs (but then again the rust doesn't bother my but I do like to test out the ABS system every once in a while