Unless you have an exotic car with carbon-ceramic brakes, then your rotors are most likely made out of cast iron, which is prone to rust. Iron oxidizes easily, and rust will form on the surface of the discs if they are exposed to water or even moisture. Besides being an aesthetic thing, rust really isn't a problem on brake rotors. On the braking surface itself, the worst rust could do is slightly modify the friction coefficient for a period of time before it was worn down. You won't notice it. Though, with one or two stops, your brake pads will rub off the rust. However, because oxidation and rust eat away at the metal, it is important to drive your car regularly and engage the brakes in order to wipe off the accumulated oxidation on the surface of your rotor. Surface rust becomes a problem once it gets deeper and starts pitting the disc.
