Most pen drives have the key component (storage board) that is encase in a plastic/fibre or a metal body. Often the rust happend at the point where we insert it into the computer and at the junction of the metal end and the encasing body where moisture or water can linger on and over a period of time form rust.
An unused pen drive does not increase the risk of a virus entry into the PC or Laptop. If the pen drive has already been corrupted then it would.
If you have any memorable data in it then the simplest thing is to use a little vinegar or warm water with baking soda. Wet the tip of a soft cloth and then wipe the rust away, simple soft brushes can also be used to scrape off. Once it is dry, then you can connect it to a spare USB cable, instead on plugging the old but important pen drive direclty. The USB cable takes the brunt of the mechanical damage.
Other way to get rid of rust is, first to gently clean the area with a home detergent solution on the tip of a soft cleaning cloth. After this, we can use isopropyl alcohol to clean and then dry it. If you are using the isopropyl alcohol, then it's wise to remember that it is inflammable. Rust removal aerosol sprays are available that you can use (Zorrick from Pidilite).
If the pen drive is not important, then you can dispose it off, why risk introducing rust/corrosion into the computer port.
If the pen drive has really important or valuable information, then I would say seek professional help instead of trying self help and risk losing the contents.