I did mine last year; same thing. It just bothered me to no end. After wire-wheel and sanding, I wiped it down with thinner, then primed it with Rustoleum Rust Converter (turns rust into black primer). Let it cure 24 hours, then 2 coats of Rustoleum black (I used a semi-gloss because I wanted to put some sort of wax on the paint). Came out nice.
Just did the underside of my basement sewer compartment, rear chassis frame, starter motot, Kwikee electric step... and sanded primed and painted the Cat oil pan. Looks so nice under there, I seem to actually enjoy laying on a creeper, just looking at it.
yea, I know... weird.