there are a number of ways to work the rotator cuff. just remember, we're talking exclusively about the EXTERNAL rotators (infraspinatus and teres minor). you are working your internal rotators already, every time you throw a football. its the imbalance in strength between the internal and external rotators that is causing the problem. so you want to focus on strengthening the external rotators, and STRETCHING the internal rotators (pecs, and to a certain extent, lats). also, as blackbeard said, some direct bicep work will help. the bicep is responsible for decelerating the arm during follow through, and a weak bicep means more stress on other structures. finally, depending on how serious you are about your football, you may want to eliminate bench pressing from your training, especially "in-season".
as far as exercises. a great one is the cuban press (keep upper arm at 90 degree abduction from the body, rotate arm forward, keeping elbow high, and return to a position where the forarm is perpendicular to the floor.) this same motion can be done using dumbells or stretch bands. also with the stretch band, keep your elbow tucked into your side, and externally rotate with the band secured to something on the opposite side, so it stretches as you "open" your arm. you can perform this same motion by lying on your side on a bench, holding a dumbell, and externally rotating from there.