Well, you know that cock is not only a word for what you are thinking about.
It is somehow likely that it comes from cock fighting pits. (roosters fighting, humans betting, you know)
Or maybe just from the position and structure the cockpit had in former times.
I don't know which is your native language, so here is the english Wikipedia entry for that:http://en.wikipedia.org/wiki/Cockpit
There is an explanation, which is unfortunately not very large.
If that Wiki entry exists in your language, feel free to check it out on the left side.
For example in german (there is a longer explanation under "Etymologie"):http://de.wikipedia.org/wiki/Pilotenkanzel
Maybe it helps.