Studies show that the hands and knees position puts the least amount of stress on a recovering shoulder. The patient can strengthen muscles and “re-tune” the joint after surgery with less risk of re-injury in this position.
However, if the position causes other problems, something different must be done. The shoulder exercises can probably be changed to a standing position with weight through the hands and arms against a wall or table. This will depend on which muscle was torn and repaired. Some muscles are more active in one position compared to others.
Putting the least stress on recovering muscle is important in the rehab of healing tendons after surgery. Too much load or force against the muscle too soon can result in a failed operation.
Bring up your concerns with the therapist and give him or her a chance to modify the program to meet all your needs.