Try some rust inhibitor...what you'll want to do is sand down those spots, apply the inhibitor, and then repaint. The inhibitor will cause a reaction with the rust and turn it into primer. The problem, of course, is using touch-up paint will be very noticeable if you sand too much. So you may want to only sand a tiny bit and see how you like the results, or talk to an auto body place to see how much it'll be to paint over the spots when you're done.