Why are aircraft callsigns pronounced over the radio in a non-phonetic alphabet way?
The FAA's ATC orders (section 2-4-20) say that the 'group form' should be used by controllers when talking to any aircraft with an FAA authorized call sign. So you would expect to hear it with airline traffic but not private flights:


  
  Air carrier and other civil aircraft having FAA authorized call signs. State the call sign followed by the flight number in group
  form.  
  
  
  NOTE- “Group form” is the pronunciation of a series of numbers
  as the whole number, or pairs of numbers they represent rather than
  pronouncing each separate digit. The use of group form may, however,
  be negated by four-digit identifiers or the placement of zeros in the
  identifier.  
  
  EXAMPLE− “American Fifty−Two.” “Delta One Hundred.” “Eastern
  Metro One Ten.” “General Motors Thirty Fifteen.” “United One Zero
  One.” “Delta Zero One Zero.” “TWA Ten Zero Four.”