Could also be Roddenberry's insistance that starfleet (some how) was not a military organization.
Kirk was the captain, also his job position. McCoy was doctor, his job position. Scott was refer to simply as engineer many times. At least Spock was never called number one.
And how would Spock have handled that old british military tradition.
"Only first names in the officer's mess, except for the captain."
Which brings up the thought that McCoy called Kirk almost exclusively by his first name - except when he was trying to make some sort of point (or being a smart ass
)! And even being an extremely formal Vulcan, Spock started calling Kirk 'Jim' quite a bit. And we all know Scotty called his captain 'Jim', exactly ONCE - under extreme dire circumstances in the mirror universe.