In early aircraft, where the plucky aviators sat was on a small bench in a (relatively large) roughly circular area within the fuselage of their flying machines.
This area looked to the interested public like the fighting pits in which one set one cockerel against another.
Hence the term "cockpit".
Given the fact that nowadays there is no resemblance whatsoever to the origin of a "cockpit" (which term I would accept were I flying a Stampe or a Tiger Moth) and given also the inevitable sni9gers and smirks that accompany the term among non-aviators, my preference is strongly for "flight deck".