You can scrub/brush all you want, the rust will just come back.
Best thing to do (what most of the Bimmer guys do) is take them off, rough them up with some 320 grit (the 3M flexible sanding sponges are awesome for this), mask off the face and paint the hat with a high-temperature light-gray paint. Most people have found that silver paints just don't have what it takes, so light-gray is the color of choice.
I suppose you could do it on the car, too, you'd just have to be way more careful with masking. I personally do it as soon as I buy a new set of rotors before I put them into storage in my workbench -- keeps the hats from rusting due to moisture in the air. I tend to buy my rotors when the particular type I want are on special at my local BMW/Porsche aftermarket shop.