Small rust spots on my paint

A. Wesley,
If they are rust stains on the paint surface, naval jelly [on eBay or Amazon] and a little elbow grease should do the trick. A good cleaning wax also works on removing surface rust stains. Work a small area at a time by hand so the applicator doesn't get too concentrated with rust. Good Luck!

A. What you are really asking is whether or not these spots are from your vehicle body rusting through the paint, or some other source. If the rust is from your vehicle body, you are seeing the results of a process that started some time ago; the rust underneath the paint has gotten bad enough to 'poke' holes through the paint. Obviously a nasty situation, and will require replacement or refinishing of the body panel.
Another (and lets hope, more likely)possibility, is that the rubbing pad/rotor have deposited metallic particles on your fender, and those particles are what are rusting. The particles from the rotor are no doubt metallic, and many brake pads are also of a metallic composition. Road gunk/dirt/moisture has allowed these particles to stay on the fender and rust.
In either case, a good washing followed by a waxing is in order. If the metallic particle scenario was the case, you should not see any ill effects from the whole thing. If it is indeed your panel that is rusting, you will likely see tiny black dots where the rust was before. You have just removed the top layer of rust that was poking through the paint, and you are now seeing the fresh rust.

A. You should be able to find a Clay bar to clean the paint.

3These are usually available in the automotive section of a large store or an auto parts store. Clay bars are able to remove metal particles and other contaminants that have become attached to the paint. Some examples are metal particles from brake rotors or rail dust.