The chief thing that you need to do is to wear a good backpack, and to wear it properly.
Whether a backpack is used by a hiker, a traveler or a schoolchild, it should fit the person, be worn on both shoulders and not be used to carry too much weight. An overloaded backpack not only puts too much pressure on the shoulder, it disperses extra weight on the hip, knee and ankle.
As noted by Julian above, a waist band can help distribute the weight into your hips and trunk. Also, make sure the straps are tight (but of course, not so tight that they're cutting off circulation). If they're loose, the bag will hang backwards, which will not only put strain on your shoulders, but also displace the weight into pushing your hips forward, taking you out of proper posture. Lastly, make sure that the straps are padded, and that the padding isn't worn out.
Yes, the rotator cuff is involved in carrying the backpack and there are exercises:
Shoulder exercises can strengthen muscles, promote range of motion and stretch muscles that are tight. The rotator cuff stabilizes the shoulder, and it is important to strengthen that group of muscles. Internal and external rotation are good exercises for the rotator cuff. Stand near a wall. Bend the elbow to 90 degrees and keep the elbow close to the body, with the lower arm parallel to the floor. Press the palm into the wall for 10 seconds; repeat on other side. For an external rotation, follow the same steps but use the back of the hand rather than the palm.
They also suggest shoulder shrugs and wall push-ups to stabilize your scapulae:
To help stabilize the shoulder blade, stand with your arms at your sides, holding a light dumbbell in each hand. Your palms should face the body. Keep your arms straight and shrug your shoulders upward toward the ears. Pause and lower the shoulder; repeat 10 times. Wall pushups are another shoulder exercise. Stand about 18 inches from the wall. Place your hands at shoulder level with palms flat on the wall. Slowly lower yourself toward the wall, then return to the starting position.
Lastly, you might simply want to be carrying less weight. A common figure thrown out (often credited to some website entitled "The Athletic Advisor") is that a backpack should not weigh more than 10% of your bodyweight. So if you're under 250 lbs, you may be overloading yourself.