Most injuries occur from a combination of overuse and incorrect technique. Home exercisers are especially vulnerable because they often begin a program with muscle imbalances which, if left uncorrected, eventually lead to injury.
Part of my job as a personal trainer is to completely assess a client before prescribing a strength training program. They are placed through a series of posture assessments, flexibility assessments, strength assessments, and core function assessments. The core funtion is key, especially transverse abdominus function. The transverse is your own natural weight belt and if it is dormant, you might as well hang up your barbell because the potential for injury is huge during deadlifts and bent over rows. All of the forces will be absorbed by the spine if the transverse cannot stabilize the exercise.
That said, the deadlift is one of best exercises for the glutes, hamstrings and low back providing the core is functioning properly. While the medical community may disagree with the sports therapy community on the risks to benefits, the deadlift has been used in successful rehabilitation of the low back, providing the transverse has been brought out of it's dormant state and can act as a stabilizer . Unfotunately, the deadlift has a bad rap due to improper technique, muscle imbalances that make it impossible to do the exercise properly, and poor core funciton vital to spinal stabilizaiton.
Why did you single out the deadlift for the source of your shoulder injury? Was the weight too heavy?? The shoulder is a very unstable joint despite it's mobility, therefore, any exercise that places the shoulder in extreme ranges of motion can cause injury (as bringing the arms too far back on the pec deck machine).
-Roe