My ford mustangs water pump is rusty

Are you referring to rust on the outside surface of the pump? Manufacturers of parts save $ by not painting their parts to prevent rust. Although I think this is wrong, and puts the quality of their parts in question (what other short cuts did they take in manufacturing to save a few cents?) this is nothing to worry about, it just looks bad. If you are referring to rust INSIDE the cooling system, it should be flushed out thoroughly, and a 50/50 mix of anti-freeze and water used to refill the system.