Hello Mark,
With some fine steel wool, you can burnish up the rust a bit, then mask of the cover where it sits and spray paint it.
If you're not too into the look of painting over your screw heads, plain old clear lacquer will work just fine and not look unusual, you will just have to continue rubbing on that transformer cover until it looks appealing.
If you're feeling very adventurous, you can move your masking down and lacquer the transformer lamination stack as well.
-PB