YouTube HTML5 / MPEG-4 videos play natively, they don't use any plugins. So what's to stop here? If you hit on a Flash movie, Safari will ask for a confirmation.
PS ClickToFlash has a killer feature - direct AirPlay of any web-embedded video! So I had to re-enable it.
The Safari power saver is fairly smart. It will only disable plugins if they aren't central to the content of the page.
A video on YouTube is central content so it auto-plays it. A flash-based ad in the corner on a news website is not, so Safari power saver will kick in.
So far it's been fairly smart in my experience and I've not had to click to play anything I actually WANT to see.