Sounds like the stain was carried in water. Could be dye based. If you can't remove it, the fiberglass tub is not too hard to refinish. As a last resort, you might try a little acetone in a very small spot. Acetone will slightly activate the gelcoat finish of the tub and will remove almost any solvent based surface stain. It won't etch or dissolve the tub, but will soften painted finishes.
If you decide to refinish, use the acetone wash, sand with 220 paper and use acrylic lacquer spray paints.