For simulating rust I use a product called "sabitennen".
http://www.work-web.co.jp/cata15_fra.html
A similar product should be available from your local model-train shop or LHS.
Another cheaper and easier option might be to spray the whole body first rust coloured and than the body-colour, to show the rust in spots use fine sandpaper and sand through the body-colour till the rust colour shows through.
Weather after as appropriate and you should be set.
I use this technique as well to show paint coming of fresh new metal, substitue rust colour with appropriate metal colour.