Medical science wasn't very advanced in those days. When the doctor is called by Reverend Parris to treat his sick daughter Betty, it's not surprising that he's unable to help. The doctor tells Parris frankly that he must look to unnatural causes to find out what's wrong with his daughter. This comment reveals that there was often a fine line between science and superstition in the seventeenth century. Despite being a man of science, the doctor is as convinced as everyone else of the existence of dark, evil spirits bringing illness and disease.
At the same time, we must also recognize that the doctor is anxious to maintain his good name as a medical practitioner. The last thing he wants is to be thought incompetent at his job. The doctor is one of just many authority figures in the play—including Reverend Parris himself—who encourages the belief that witchcraft is responsible for every misfortune, largely out of a concern to maintain social status and reputation among the townsfolk of Salem.