When used in a
civil aviation context, the
flight deck is another term for
cockpit. In other words, it is the location inside a large aircraft from where the aircraft is controlled. This is typically restricted to airplanes which are large enough to have multiple decks inside them, even if the flight deck does not occupy an entire level by itself. It is possible that this use arose from the large
flying boats of the early twentieth century, which (when at rest) were essentially ships or boats. In that sense, the use of 'deck' is obvious.
When used in a nautical context, the flight deck is the deck, or level, of an aircraft carrier on which flight operations occur. On American CVNs, the flight deck is placed at the top of the primary hull of the ship, with only a small section of the ship protruding above it for control purposes as well as the mounting of masts for sensors and communications gear. That section of the ship is called the island, and on American-model carriers is roughly one-third along the hull between stern and bow on the starboard side of the ship.
It wasn't always this way, however. Early aircraft carriers, when they were little more than a concept, were built by converting existing cruiser hull construction for the purpose. Because the typical warship had no flat surfaces on its hull, the flight deck was constructed by building scaffolding above the ship's superstructure and placing a flat deck at the very top, held 'above' the rest of the ship. This was sub-optimal from a design perspective, as it not only made the flight deck vulnerable and difficult to get to, but raised the center of gravity of the ship, making it easier to capsize and harder to properly ballast. It also, of course, meant that aircraft had to be both operated and stored entirely on the flight deck, since there was no appreciable structure directly beneath it. This limited the carrying capacity of the ship and made flight operations much more complicated.
The Imperial Japanese Navy, just prior to World War II, adopted a slightly different configuration. Their aircraft carriers, including the ones which carried out the famous strike on Pearl Harbor on December 7, 1941, had no structure above the flight deck, but also had the flight deck mounted lower, with abbreviated superstructure beneath it. This allowed for the use of the ship's internal volume to store the (fragile) aircraft through the use of elevators which could raise and lower them to and from the flight deck. These ships' lack of superstructure above the flight deck led to their being nicknamed 'flattops' by American military personnel .
The flight deck, originally and through World War II a relatively simple surface, became suddenly much more complex with the advent of the catapult carrier. Although propeller-driven aircraft can typically lift off a carrier deck entirely under their own power, heavier jet aircraft with higher performance and hence higher stall speeds needed extra help. Designers began to place steam catapults within the structure of the flight deck, which allowed these aircraft to be 'flung' off the deck.
This, of course, meant that the flight deck suddenly became a much more complex mechanism. Modern carriers have as many as four catapults in their flight decks, as well as armor surfacing to prevent this enormous target from suffering damage at trivial incidents and disrupting the ship's operation. Elevators are integrated into the flight deck, as are hydraulic jet blast deflectors to protect personnel and other aircraft from the jetwash of airplanes leaving the carrier. Entire ILS installations are embedded in the flight deck and its surrounding structure. Firefighting systems, refueling systems, anchoring and tiedowns, and a myriad of other bits make the modern flight deck a serious machine in its own right, rather than a simple teak-wood surface as it once was.
The flight deck of a modern operating carrier is also a horrifically dangerous place. Jet aircraft operating within feet of other airplanes and people; tow vehicles, jet fuel, munitions, catapults, arrester cables and associated hydraulics coupled with the everpresent ear-splitting noise all conspire to make this area lethal to untrained (and, sometimes, trained and experienced) personnel. One of the most complex pieces of the modern carrier isn't the technology itself, but the routines and procedures adopted by the deck crew to ensure that their tasks are performed as safely and quickly as possible. When a new carrier is commissioned, one of the first things that happens is the first deck crew evolves its own set of rituals and routines - one informed by the standards and manuals of the U.S. Navy, but one that is also unique to the ship - for carrying out flight deck ops. These routines, and the procedural and institutional knowledge that is embedded in them, is one of the great assets of any Navy's carrier aviation department. They are much, much harder to devise and perfect than it might seem at first blush, and every change in the ship's design and systems (or those of the aircraft it services) requires adjustment in these routines, often worked out or perfected through trial and error.
When you are walking around someplace with ear protectors on, and thirty-ton objects with flamethrowers on their rear are being accelerated from zero to over one hundred and fifty knots in a few hundred feet, the danger level should be obvious. When those objects cost upwards of a hundred million dollars and carry all manner of deliberately explosive and pyrotechnic objects which are designed to be dropped off of them, well...heh.