A pilot was an individual who navigated an aircraft, ship or starship.
A command pilot was a navigator from the command division on a starship.
When Leonard McCoy and Spock were arguing over who ought to fly a shuttlecraft into the space amoeba, Captain James T. Kirk broke up their spat by indicating his desire to go instead, as he was a better command pilot than McCoy. (TOS episode: "The Immunity Syndrome")
A fighter pilot or combat pilot was a military aviator explicitly trained to engage other aircraft. On the planet Earth, fighter pilots were used by the governments and militaries of many countries during the 20th century.
The Battle of Britain, an aerial conflict between Germany and Old Britain during Earth's Second World War, utilized fighter pilots on both sides of the battle. The Battle of Britain was one of Julian Bashir and Miles O'Brien's favorite holoprograms at Quark's holosuites, taking the role of two RAF pilots in a squadron that included Clive. (DS9 episode: "Homefront")
In 2373, Elim Garak lightly chided O'Brien for "spend[ing] hours in the holosuites dressed up as [a] fighter pilot, reliving ancient battles", implying that despite his current occupation as an engineer, he was still a soldier at heart. (DS9 episode: "Empok Nor")
In 2375, Bashir proposed a toast to Starfleet helmsman, Lieutenant junior grade Hector Ilario, after he successfully evaded six Jem'Hadar fighters while at the helm of the USS Defiant. He said he was "living proof that Starfleet Academy produced the finest fighter pilots in the galaxy". (DS9 episode: "Field of Fire")