I'm not sure we are talking abour rust here - sounds more like brake dust. Different compound brake pads affect dust levels.
The brake rotors (not the hubs) can rust up, as the are make of materials that rust very quickly. Most brake rotors will have rust on the edges - this is normal and doesn't transfer to the wheels.
Some rotors also have bare metal centres, which rust very qyuickly and look nasty but once again this is normal and once they have a layer of surface rust, they stop rusting adn this rust doesn't normally transfer to the wheel.
I recently installed new rear rotors and pads and the new rotors did not have painted centres, so I painted them before installation.
I have also removed, cleaned up and re-painted existing rotors in the past.