If you have a Dremel, use the wire brush attachment and remove all the rust. If not sand or steel wool the spot clean carefully.
Then go to a car store and buy a tube of touch up paint that comes close to your bike (a paint chip always help). I always buy a tube of clear coat too.
Dab some paint on and let dry. Add another coat and let dry. Put on a coat of clear coat.
This works great for small rust areas.
I have also heard of people using nail polish but I haven't tried it.