A beaker full of death wrote:
Let's face it, the usage in modern Trek stems from the ignorance of the writers.
Or, as has been discussed here, from the deliberate choice of the writers to use the commonly used civilian connotation of the term as a way of indicating that the Enterprise
was the best of the best, on the basis that Starfleet is not our navy or any navy and that by the 24th century, things change. Things the writers do differently from the way we would do them do not have to flow from ignorance. They can simply be choices.