Rust is almost a natural thing with muzzleloaders as blackpowder and pyrodex is corrosive. The only thing you really have to be careful with is the threads that hold the nipple in. You get too much rust on that and you can shoot the whole nipple assembly into your eye. VERY IMPORTANT... inspect the nipple and the threads for any excessive corrosion or damage. If there is, the barrel and nipple is unsafe and should be discarded
If it's inside the bore, use a Hoppes Tornado brush to take out as much as you can and then inspect the bore. If you still see the grooves and they are distinct (be sure to look for major rust pits and craters or anything that might consitute a weak spot in the barrel) just go ahead and oil it and shoot it. Care for it promptly after shooting and in a few sessions, you will wear the rust away.