I had a protruding disk when I was 17, dont wait, do something now! Back pain usually does NOT get better on its own. If you must do physical therapy, and the pain increases dont hesitate to stop it and get your doc's attention! Make sure they do more than just x-rays too, they are usually inconclusive. An MRI is your best bet for identifying the problem. Dont give up until you get a difinitive answer too.
Good luck!