Ogg has advantages. Flash for video delivery has major disadvantages
Those poor disadvantaged guys at YouTube. They're disadvantaging all the way to the bank
I'm certainly not pushing Ogg here, but... Flash video *does* have disadvantages, most notably in terms of quality.
YouTube chose Flash video as a least common denominator. Flash is ubiquitous, and, ultimately, cheaper in terms of bandwidth. In YouTube's case, they wanted to make their videos as easy to use/view as possible as cheaply as possible.
That doesn't mean Flash video is always the best choice.