Starfleet seems to use a naval ranking, and officers use words like "hail", "heave to", "away team", and "bearing". The navigation terminology in Star Trek sees to be related to the galactic plane, which again evokes the surface of the sea.
The drive section of the Enterprise looks like the keel of a boat to me, and her nacelles look like the hulls of a catamaran.
Roddenberry loved the Hornblower books and I'm sure he was influenced by naval aesthetics.