Check out DuPont etching primer to cover bare metal. This is what is used in body shops that use DuPont products. You can get it in a spray can for small areas, but when using it be sure to allow ample flash time between coats (follow the directions on the can for temperature and time between coats). PPG also makes really good etching primers for covering bare metal. Also when using an etching primer you want to follow up with a filler primer (which needs to be sanded and blocked out after 2 hours of drying) then followed by a sealer to prevent rust from coming back again. After sealing the filler primer you can then apply base and clear coat. You can purchase these products at your local auto body supply store (in the Seattle area we have Westco).
And also as a good rule of thumb, try not to get etching primer on bondo, it tends to cause solvent popping/pin holes.