I was reading The Smoking Gun's 2003 Article of the Year and I came across this page which explains the origins of lots of other naughty words:

Cock:
The word "cock" dates to early 17th century England and not to surprisingly relates to the rooster. Roosters have an annoying habit of getting up early in the morning and crowing loudly to welcome the morning sun. As the rooster crows, he stretches out his neck and points it upwards. Think, morning. Think something raising it's head....enough said?