In order to paint over rust, you should prep the area by scraping off any loose rust. Paint alone does not adhere as well to rust and when it does stick, rust stains can bleed through the paint coat and discolor it.
Typically for rust, you do not want to use a latex (water based) paint because it may cause the metal to rust more and will bleed through and stain the paint.
Additionally, a primer specific to your amount of rust will help aid adhesion. For extensive rust, prime with an oil-based rust conversion metal primer from a brand like Sherwin-Williams or Rustoleum. If painting over lightly rusted or bare metal, prime with a rust-preventative metal primer. A primed metal piece can be coated with either water or oil-based metal paint. Some paints, called DTM (Direct To Metal) are designed to encapsulate rust and prevent it from spreading. It is best to talk to a knowledgeable paint supplier or professional painting company to ensure you are using the correct product.
