What makes me think companies with the concerns outlined by the OP would not consider HTML5? It would be much more difficult to control their content. Flash is great as a hard to penetrate content container. Exposing your content by using HTML + JS to display it is less than ideal if you want to serve ads/make it difficult to steal content.

Youtube streams the file. Youtube also serves ads. Youtube, as exemplified by the OP and by my link is experimenting with an HTML5 player. But you are right. HTML5 has this problem of exposing the player, so any mechanisms in the javascript to force ad viewing can be more easily defeated.

A possible solution would be to track user session and force a new ad on every new session (so you can't clear cookies). That way ad tracking can persist outside of the video player itself by using the cookie.

The other problem is, who serves video files themselves anymore? So if Youtube, or any other video services who depend on ads to keep themselves afloat can't use the HTML5 video tag, who will?

It seems to me that unless the ad is prepended to the actual video file then using javascript we can tell when an ad is playing and kill it/skip to the "real" content. On the other hand the average user probably does not have the expertise to kill ads, so maybe the point is moot.

Or use firebug and inject javascript into the page.

I think people stopped embedding videos and started using third party tools because it makes it easier. Third party tools will always make it easier. No need to worry about bandwidth, file space, etc (even if the cost of these items are going down). And as long as these tools make it easier, these tools will probably want control of their players and will want to put ads in them.

No they don't, they use progressive download. This is very different from streaming.

Actually it'd be more in YouTube's interest to control the playback experience since they use HTTP streaming, since the stream is less controllable by itself.