For those unfamiliar with SS, it gets its stainless quality from a coating that forms on its surface. This is what is referred to above as passivation. Clean, dry stainless will passivate itself, unaided, in a week or two in a clean, dry environment. Drying after a rinseless acid wash will greatly reduce the time needed, depending on the acid used. In industrial settings, nitric is the acid of choice.
Get the rust off first. As Sam H points out, touching SS with any kind of mild steel embeds mild steel particles into the SS, causing rust. A good hardware store will have SS-wool. They'll also (in the USA) have a product called a 'Scrubbie', available in SS and copper. Green Scotchbrite pads are good, but red ones are better (scratchier). Look real hard and you'll find dark gray ones meant for SS.
Use Comet, if you have to, but rinse it well afterwards. Comet contains chlorine, which will cause pitting on SS surfaces. There are cleaners meant for SS: Zud and Barkeepers Friend are often available in hardware stores. These cleaners will contain oxalic acid. Acid good, chlorine bad.
Is the rust in cracks and corners? Try Naval Jelly, or an acid soak. Phosphoric acid is preferred, as it's not as nasty as nitric. I've seen it in hardware stores, but not very often. I suppose citric or even vinegar will work, too, but I've never used it. Warmer (120-150F) works faster than colder.
Unsubstantiated anecdotal knowledge: packaged beverages are made infection-resistant by making them acidic, usually with citric acid. I've been told that Coca-Cola uses a lot of phosphoric acid to achieve this effect. I've always meant to drop a rusty bolt into a glass of Coke and see what happens.
There's no need to put any kind of coating (WD40, wax, etc.) on SS. Clean, dry SS is happy SS.
Charley