The active ingredients in car rust remover are what eliminates the rust. In commercial car rust remover, the active ingredients are toxic acids, like hydrofluoric acid, phosphoric acid and oxalic acid. Due to the corrosive nature of these acids, the utmost caution should always be taken when handling commercial car rust remover. If you are doing repair on your own, wear gloves and protective eyewear.
For more info, see How to Repair Rust on Your Auto Body.