Many times rust will come from the back side of the metal. If the back side is not treated it will come through anything you put on the outside. It is all but impossible to realy clean all the oxidation from behind a panel, plus there is usualy a problem with the car either retaining dirt or water behind a panel that rusts. Dirt will hold moisture and make it rust faster. Always check your drain holes in the bottom of your doors and under the rocker panels when you get a chance or are doing a real good wash job. If the panel has rust spots on the outside from say a door chip that went through the layers of paint. Proper cleaning and a primer (not the spray can kind) to seal the metal and prep it for paint then a good paint to top coat it should stop the rust. Primer by iitself does not stop moisture as witnessed by primered sections on cars rusting through the primer. It has to be top coated. Primer is used to bond the paint to the metal and in some cases add an extra layer of rust protection such as zink.
Hope that helps,
Dennis