Unfortunately once rust starts there's no way to really stop it without major surgery. You can try a rust inhibiting primer or there's a rust converting type of coating that's available from the local body supply shop. Just sand the affected area, front and back, as good as possible then brush on the coating. It'll convert the rust by stopping the oxidation that causes it. If the metal is coming apart, you can then repair the area with fiberglass, prime and repaint. If it's still somewhat solid with mostly surface rust, just sand it smooth, apply the coating, prime and repaint. It's not a permanent fix but it should buy a couple more years for your rig.
Is it surface rust or are there holes? If its just surface rust you can get this wheel from 3M. Its grey and kinda looks like a sponge. You put it on your drill and use it to remove the rust, then just prime it and paint it. One other route you can go is check with a Line-x dealer to see how much they would charge to coat them.
We had the issue on a 99 and when we checked Ford only sells the rockers as a complete piece that surrounds the entire cab opening. We found some aftermarket ones through LMC . I think they were about $600 plus paint and install. Not a cheap fix but really the only one worth while long term.