If its just surface rust, sand it down to as close to 'proper' metal as you can and the use some Kurust(hammerite) sparingly to get rid of rust...
Once the Kurust has cured, paint over the whole rack with some black metal paint to make it look tidy (if you really wanted to do a job, use a zinc primer, although i think it'd be over kill for a roof rack)
(To be honest, if its an old rack just sand it off or get rid. If its properly rusted then the only way to get rid of the rust is cut it out and it wouldn't be worth it imo, for the sake of another roof rack)