Brake rotors rust... That's all there is to it.
They are just bare metal for the pads to grab onto, as soon as the car is parked and water gets on them you will see rust. Then once driven again the brake pads will remove the rust. Not a big deal.
i've heard of people buying new rotors and painting them (any color with caliper paint) and then once you use the brakes for the first time it rubs off the paint where the pads hit...looks pretty cool from what i hear, and since the pads always rub the rotor on the same place, you don't have to worry about the rust...
Another alternative to Caliper Paint is using BBQ Paint and doing them BLACK https://www.celicahobby.com/ubbthreads/thread.f_56923_0_collapsed_2__1.html