Why is it customary to call people with doctoral degrees doctors but not people with masters degrees masters? Why is it customary to call people with doctoral degrees doctors but not people with masters degrees masters? They are both graduate degrees that supersede the undergraduate degree.
If you're talking about the use of doctor as a title, as in "Dr. Smith", I doubt there's any compelling explanation.  Most degrees don't come with titles: nobody say Master Smith or Bachelor Smith or Associate Smith.  Historically, magister (corresponding to the master's degree) was just as appropriate a Latin title as doctor was, but it simply isn't used in modern English.  These titles are nearly gone, with just one remaining.  It's probably no coincidence that the last remaining title is also the fanciest, but that's just speculation.

Even for the doctorate, the use of the term "doctor" has degenerated to the point where in English it can only be used as a title, and not as a general noun.  If you say "my friend John Smith is a doctor", practically everyone will assume he's a medical doctor.  You could only get away with the more general usage in the narrowest academic context, and even there it would be considered pretentious and archaic.