But with Flash, H.264 is guaranteed to be supported. regardless of what browser is used. Flash is a sure bet compared to HTML5. Also, H.264 is much better than Theora (better quality, lower bandwidth). I'd hate to see sites using Theora.
Furthermore, it will take time for all users to switch to HTML5 browsers. I suspect that HTML5 will not be a real option for at least the next 6 years.