I don't really mind Youtube (or Apple Keynotes, Quicktime Movie Trailers etc.) not using royalty-free codecs that much. If every web decision was made through the lens of "is this image format suitable for Flickr", or "is this text encoding suitable for Wikipedia" then you'd end up with a very strange kind of web. Youtube seems to be regularly predicted to kill the internet as a whole anyway due to its size and popularity, with or without Theora.

If anyone is going to make extra work for themselves by using multiple codecs, or be subject to licence fees then it should be the giants of the web, not folk uploading videos of their cats to their blog (a demographic for whom Theora is a perfectly good solution if it was supported by Apple and Microsoft).