Oxalic or Muriatic Acid diluted with water will remove rust stains from a roof.
Here in Tampa, Muriatic Acid is common, used for swimming pools.
Diluted 1 part acid to 4 parts water, it will remove rust stains off a roof.
Plain Vinegar is a mild acid, and should be tried first!
You may have to apply several applications of it, but we here at Apple Roof Cleaning Tampa suggest you try it first ?
More roof rust stain removal info may be had by going here http://roof-cleaning-institute.activeboard.com/