According to the OED the word predates aircraft significantly as it's actually a sailing term.

http://www.oxforddictionaries.com/definition/english/cockpit

Late 16th century (in sense 2): from cock1 + pit1. sense 1 dates from the early 20th century and derives from an early 18th-cent. nautical term denoting an area in the aft lower deck of a man-of-war where the wounded were taken, later coming to mean 'the ‘pit’ or well from which a yacht is steered'; hence the place housing the controls of other vehicles.

What isn't clear is whether the etymology comes from cock as in rooster or if it refers to cock as in a valve. Both are logical in this context.

http://www.aerospaceweb.org/question/history/q0064.shtml Follow the origin through cockfighting rings to the lowest pit around the stage in a theater to the lower deck of a ship (mentioned in the Oxford link).

"In addition, the rudder control space from which a vessel is steered is sometimes called a cockpit since a watchman in the highest position is called a cock, and a cavity in any vessel is called a pit.

This sense of the word, as an often confined space used for control purposes, was first applied to an aircraft around 1914 by pilots during World War I. In keeping with this same meaning, the tightly confined control space of a racing automobile also became known as a cockpit by about 1935."

According to the online etymological dictionary:

cockpit (n.) 1580s, "a pit for fighting cocks," from cock (n.1) + pit (n.1). Used in nautical sense (1706) for midshipmen's compartment below decks; transferred to airplanes (1914) and to cars (1930s).