Maybe the encomium is used to distingush the doctor from a quack or a witch doctor. :)

Actually, the term "the good doctor" brings to mind the venerable salutation "my good fellow". It's a sign of respect, wouldn't you say?*

Doctors represent the only traditional profession which commands any respect in the estimation of the average citizen nowadays, and even that respect is a pale shadow of what it once was when the term "the good doctor" was in vogue in much simpler, less litigious times. In those days, doctors made house calls and received payment in kind more often than with money, particularly during the Depression.

Back then, being a doctor was more of a calling, like the priesthood, than a profession.

* Good
Dictionary.com

6. Worthy of respect; honorable