Had an issue with rust not on wheel rims, but on the lower control arms of my '09 S model. At the time, the big news--along with unintended acceleration--was the frames rusting out from underneath Tundras. I freaked a little, took it to a dealer, and received no word on the issue. So, I cleaned the areas with a cleaner made to eat rust away, and sprayed them with satin-black Rustoleum. So far, the rust has not reappeared.
My opinion is that the paints used today are made to be so "environmentally friendly" that they're no earthly good. It is also possible the car had been driven in salty conditions (as in wintertime).
Your rims may be rusty on the inboard sides, too, so it may be best to remove each rim, sand them, and--being sure to protect the tires--treat both sides with a chemical rust remover (
I used this one), then paint with satin-black Rustoleum.
