I heard somewhere that it is important to your prostate to make sure that you masterbate at least once every two weeks, and if your doctor told you to do physical therapy for the prostate and didn't tell you to do anything else then he must have thought that it would be enough.
If you still are having problems after you've tried what your doctor suggested then go back and tell him.
Ps. Why stop masterbating anyways, it helps with stress and just generally feels good, just don't go to far with it :)