I can't see the rust stain your speaking of, but I wouldn't start with removing the coating in order to get rid of it. I have used Lime-Away toilet bowl cleaner gel on tough rust stains on items other than just toilets. I apply it and let it sit for a minute or so, and then use a non-scratch (blue) Scotch Brite scrubbing sponge. read more
First off, modern enamel tubs are not very scratch resistant. Anything you do with sand paper or a pumice stone will probably leave a mark. A fairly safe alternative, that may or may not get rid of the stain, is a paste made of baking soda and hydrogen peroxide. read more