Probably because they haven't implemented all of the same features in HTML5 as they have in the Flash version, such as ad overlays and annotations. It's up to the person posting the videos whether or not to use these features, and if they do, it forces the player to use Flash.
That's because of the ads. With things like ClickToFlash or youtube-dl, you notice that most videos are actually available as MPEG4 and/or WebM.