I don't recommend rubber for several reasons. Metal covers are available that snap around mid-pto and rear pto shafts. These covers are shields, not sheaths.
Rubber has a tendency to shrink, and that can make removing it a real PITA. Cutting it off is often the only resolution. Rubber and cloth tend to stick to each other, usually when the rubber thing is turning. That can make your gloves, shirt sleeve or pant leg get wound up in it before you realize what has happened. Yes, pto levers can get bumped and safetys shortcut. You don't get too many true believers admitting they just had a close call. The ones in the Emergency rooms missing an arm give the best support for this suggestion. Yes, its just a stub shaft, but all these tractors would really like to kill you.