The origin of the term "Jolly Roger" is not likely to have derived from the supposed French "jolie rouge", 'pretty red', because pirate flags did not come into common use for many years; and in any case the red flag of piracy was infrequently flown. The far more likely source is that the English commonly named their stud bulls "Roger", this word already being a term widely used for sexual intercourse, usually of a vigorous nature. One of the characteristics of pirates was their brutal treatment of female prisoners, who commonly were 'rogered at the rail' by one and all and then thrown overboard, to fend for themselves.
The supposed history of the Jolly Roger is of a one with that old-time favourite of writers of piratical stories, "walking the plank". In fact there is no evidence that pirates ever made their victims walk the plank; there was far too much sport of another kind to be had. A favourite method of dealing with prisoners was to tie them to the mast and then pelt the unfortunate victim with broken bottles. Many other cruelties were also employed. The life of a pirate was, above all things, exquisitely wretched and boring; such that when prisoners were taken there was much gleeful anticipation among the pirate crew regarding the entertainment in store for them. It is most curious that the piratical life - nasty, short, and invariably brutish - has been so romanticised by literature.