It's not only necessarily your rotator cuff muscles, it could be any one of the smaller / secondary supporting muscles in your shoulder....as was said previously, if your secondary muscles are weak, as your major muscles get bigger and stronger, you will inevitably injure yourself....
Also, if you have a very or over-developed back, muscles will tighten up severly causing knots and eventually pain & injuries... you need to keep your upper back and shoulders very limber.... do warm-up exercises several times a day, especially prior to any workout (even if it's not shoulder-related) .... see a good sports chiropractor if possible.... adjustments help... plus they can recommend some good exercises... you can also do a search online for a wide array of shoulder / rotator cuff exercises.... finally, ice the pain for 15 minutes several times a day