Sorry to hear that it is rust. If it weren't, the best Chrome polish I've ever used is called Neverdull. It's some sort of fabric, maybe cotton, wadded in a can. You just tear off a small piece and it will do your whole rim. When I got my rims, they had a yellowish color to them which wouldn't come off with other "Chrome Cleaners". The Neverdull took it off without any effort.
A lot of the time, rust seen on surfaces that are supposed to be almost rust free is usually metal shavings picked up from the ground that tend to rust.. from winters.. plows scraping curbs.. cars.. etc etc.