Remove any loose flakes of paint with a paint scraper and a wire brush. Keep scraping and brushing until any piece of paint that is even somewhat loose has been removed.
Apply a commercial rust remover (widely available at automotive stores) to the rusty areas on your furniture, and allow the coating to dry according to the manufacturer's instructions on the bottle.
Sand the rust remover off of the furniture. (It will turn the rust into a sort of black powder.)
Using the brush, apply a coat of the rust-resistant primer to all of the exposed areas that you have just scraped and sanded. You do not need to apply primer to the areas where you will leave the old paint. If the old paint is still firmly attached, it makes just as good a bottom coat as the primer.
Brush on a second coat of primer once the first has dried.