Now I know some people paint these after cleaning them, but why?
After using the wire brush they look like new.
Does paint clean easier in the future?
seems like it might just flake off, rock chips and then look worse.

Some use a clear coat to keep them looking like new. If you leave them in their natural finish they will return to the look that you just worked hard to get rid of

I was also reading about using a 12 volt battery charger, some re-bar and a few chemicals to remove rust from parts. I was considering putting the wheel bearing assemblies in that solution to remove the surface rust. I could then throw a coat of black paint on those to prevent future rust.
http://makezine.com/projects/electrolysis-rust-remover/QUOTE]

I would use and have used products like Metal Rescue, which is a rust remover bath. A lot easier

Ron