How to Remove Small Rust Spots from a Car (wikihow.com)

http://www.wikihow.com/Remove-Rust-from-a-Car

Note: I would also recommend finding a body repair store that will mix your exact color paint and applying a clear coat afterwards. It gives it a more polished look and comes close to matching the original. If you have large areas of rust or holes, you may want to turn to a professional  paint and body shop.