Unless you're encountering a lot of salt and water, the rust really isn't much of a big deal.

If you can sand off the rust and apply touch-up paint, great. But be careful-- If you don't get the surface prepped well enough, it can rust underneath the paint.

I have one bike that has more exposed metal than paint left on it. When a rust spot shows up, I rub a little heavy oil onto it. The oil basically "seals" the rust spot to air and repels water, inhibiting rust. For a cleaner and more permanent solution, you could probably also use wax.