Emily, yeah, pups can be hard on the rotator cuff, especially if you're doing them with a wide stance - are you doing them narrow, Pilates-style? You're right the bellies of the rotator cuff muscles are along the scapula, but they have their insertion on the head of the humerus - that's what allows them to rotate the arm, and it's why there's no bone-to-bone attachment in the shoulder socket. Here's the best
illustration of that that I've seen. The shoulder is a wacky joint, really, crazier than the knee even - be careful with it. :(