Rotator Cuff Injury

First advise would be to seek a medical opinion, perhaps a sport medicine doctor.

What type of workout are you doing: weights, throwing a ball, swinging a tennis racket?

While rest may be best for an injury, rehabbing should include flexability and weight training.

Do some research for exercises like external/internal rotation, scaption, rear deltoid raises. Strengthing the shoulder capsule is important in PREVENTING injuries. External rotation is critical as usually most people have bad internal/extrenal rotation ratios: internal is usually stronger that external and correcting this imbalance is key to a healtyh shoulder, especially if you are into throwing movements.
Here's agreat shoulder book:
http://www.amazon.com/gp/product/0944831257/002-6553025-8201617?v=glance&n=283155

Here's a link to a site with a wealth of information from a professional who deals with issues like this
http://www.houstontexans.com/fitness/fitness_corner.php
Dan Riley, who is the Texans S&C coach is THE MAN when it comes to NFL Strength and Conditioning. He was even nice enough to personally reply to a few e-mail questions I sent to him.

Wishing you well...