It's simply that Google hasn't reached a feature parity point with their Flash video player compared to their HTML 5 one. They could get there, but it's going to take some more work on their part. The team is not only responsible for the website, but also the various YouTube apps across a number of platforms. Mobile, consoles, etc. Years of development effort exist in the Flash player they use, not as much time has been spent on the HTML 5 or mobile side.

Once they can support the ads, and other features in HTML 5, it will work just fine. I don't know an ETA, but had the situation explained to me by an engineer friend on the YouTube side of the house.

Google remains an advertising company, so it makes sense that they are pushing more of their content creators to enable ads on their videos. Interestingly, if you upload a video with copyrighted music, most of the rights holders will allow you to keep it on Youtube, as long as you turn on ads and direct a cut of the revenue to the rights holder.