With respect to Flash, the issues have to do with the uses for tracking, so-called Flash cookies for example, and the fact that today, when you use the cookie controls in your browser, they don’t directly affect the treatment of Flash local storage objects or cookies.There’s some other issues with Flash that I could suppose we could address at another time.

Princeton University Professor Ed Felten via A deeper dive into Do-Not-Track – O’Reilly Radar