I don't see any implication that YouTube/Google is throwing away anything. They stated that they chose to transcode a selection of videos that the vast majority of viewers view. They didn't imply that they weren't going to transcode the remaining videos, but that they feel the number of videos that they have transcoded is sufficient enough to declare WebM as being the default codec.

Really, that statement isn't any more worrisome than the unstated fact that Google could potentially delete every video on YouTube and every single email in Gmail and Google Apps on a whim.