The arm was never designed to throw a baseball from the overhand position. The most natural way to throw a ball would be underhanded. Pitchers who pitch softballs can throw for multiple games without needing a day's rest. However, overhand pitchers need to have a minimum of three days of rest after pitching a game. 

In the overhand position, the arm is moved away from the body. The strength of the pitch comes from the legs and the torso, not from arm strength. Although you hear of a pitcher having a strong arm, it is actually a strong body that accelerates the ball. In the throwing motion, the body starts off 90 degrees from the final angle that the ball will be released. The pitcher pushes off of the ground with his leg and then rotates his body around. The arm actually acts as a whip. Just as a whip gets its final acceleration from the snap of the wrist, the arm gets its final acceleration from the twisting motion of the body. 

In order for a fast ball to go 95 miles an hour, the arm must travel 95 miles an hour. The body and the legs accelerate the arm, but only the shoulder muscles can decelerate the arm. It has often been theorized that pitchers would do less harm if they ended their pitch in a forward roll. In other words, instead of stopping the arm, the arm would simply carry their motion and the body would be used to decelerate the arm. However, I have not been able to get a single pitcher to try this as a pitching form and I do not think that it will ever happen. 

The shoulder muscles, primarily the rotator cuff, are largely responsible for keeping the arm from flying off towards home plate in the direction that the ball has been thrown. Most common shoulder problems actually come from the deceleration of the arm, not the acceleration. One of the more common throwing problems is partial rotator cuff tears that are involved with arm deceleration. 

These rotator cuff muscles are also irritated when the arm is held in a cocked position. These muscles rub directly over the glenoid bone which causes irritation as well. This combination of rubbing over the glenoid bone and being the primary destabilizer to the shoulder joint give many throwers the partial rotator cuff tear that is most commonly seen. 

Another problem with the shoulder is that pitchers have more laxity than the normal athlete. Pitchers are able to externally rotate the arm so that the hand starts further beyond the ear than the normal thrower. This increases the starting point of the arm which allows the arm to accelerate even more with the rotation of the body. Furthermore, this laxity allows the shoulder to come out of place just a slight amount as the arm moves forward and the ball is thrown towards home plate. This sliding out of place also adds to the problem of putting more pressure on the rotator cuff. The rotator cuff is used to keep the shoulder in place. Therefore, the rotator cuff has two functions during the throwing motion. One is to decelerate the arm and the other is to keep the arm from sliding out of place and flying off to home plate in the same direction as the ball. 

There is a new treatment for throwing shoulders that has been employed within the past year. In order to keep the arm from sliding out of place, an arthroscopic radio frequency probe is being used to "tighten up" the capsule of the shoulder. This procedure has been used in a number of celebrated athletes including Doug Johnson as well as Greg Norman. Although the long term results of this procedure are not in yet, the initial results show that this arthroscopic procedure can tighten up the shoulder joint and allow the athlete to return to throwing quicker than an open operation.