Why do we put so much emphasis on muscle rehabilitation, especially isometrics?

Cuz u need it. Early muscle activation after an injury or surgery has been shown to accelerate recovery. When we need to protect a repair then often isometrics can be done safely, while in time more motion will be appropriate with your workouts.
Stable joints... Strong muscles lead to stong healthy joints; and isometrics is a great way to strenghten muscles while being joint 'friendly'. It's a win/win situation depending upon what one is trying to rehab; discuss the matter with your doc/physical therapist for more info. Cheers!