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A Captain is generally the commander of a single 'unit' in whatever service he serves in. In pre-industrial militaries a Captain might command a column of soldiers or a single sailing ship, both relatively equal posts in terms of human lives under one's control. However, as militaries developed the ship got bigger and the Captain stayed in command. Bigger armies on the other hand just got more Captains.

Captains in Star Wars

In the Imperial Starfleet, a Captain is generally in charge of a single ship, such as an Imperial Star Destroyer, and is responsible for any and all screw ups that happen on board it. Lower-ranking officers command smaller ships, but may be addressed as Captains out of respect.

Flagship captains, such as the captain of the Executor, must always defer to their superior, but they remain in charge of the day-to-day running of the ship.

Captains in Star Trek

A Captain of the Federation has similarly wide-ranging powers due to the long durations that he may spend distant from his home port. However, his ship is proportionally much smaller.