Rust gets started at a break in the paint, which lets moisture reach the iron molecules in the steel panel. If you only cover the break with paint, the reaction will still continue without fresh water, using atmospheric oxygen. It is necessary to either mechanically remove it with sandblasting (a bit messy) or chemically stabilize it.
Chemical rust converters, such as Extend, from Loctite, transforms red, flaky rust to a hard, dark-gray compound that prevents further rusting and forms a stable base for paint. Before using a chemical rust remover, you should scrape and wire brush away as much of the flaky rust as possible. Remove any oil or grease from the area with a solvent such as lacquer thinner. Then wet the area with rust remover, keeping it wet for about 2 hours, and hose away the residue. For stubborn rust, you might need to cover the area overnight with rags soaked in rust remover. Lastly, brush on a coat of converter following the instructions on the label. Once this is dry, the area is ready for painting.