If it's just surface rust, sand it off and coat the bare metal with POR15. Level the surface out with a bit of fibreglass filler, and then prime and paint. It's a time consuming process...so take your time with it.
The POR15 is an important step. I've been using this product for a while now with good results. It's a rust preventative paint. It will stop rust from spreading or getting worse by isolating it from water and oxygen (needed for oxidation to occur). Normal paint does not offer this kind of protection. However, the product is not cheap, and it does have quite specific application instructions that need to be followed carefully. If you have any questions about the stuff, feel free to ask.
Are you sure its surface rust or is it coming from the inside out? Either way por15 rules every honda owner should own some. Works great on sunroofs and door bottoms also. Used to praise the stuff on the resource before Steve put an end to my membership. I have used it on my rear 1/4s with much luck and doors and sunroof still over a year later its just fine. Used the green fiberglass bondo over top of it.