So far we’ve already transcoded videos that make up 99% of views on the site
or nearly 30% of all videos into WebM
There really isn't much of a long tail on YouTube, it seems. It's sort of worrisome that google could throw away seventy percent of the videos with the vast majority of users not caring.
The vast majority of video views (99%) would be unaffected but that doesn't imply that the vast majority of users wouldn't be since most users are going to view way more than one video.
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.
That's the wrong way of looking at it. Most people upload stuff few people care about. Their is a large number of people who cater to a small community, and YouTube makes sharing videos easy for that community. A low number of views doesn't equate to low interaction, either.
Take a hobby of mine: miniature painting for $40k. I published battle report videos, painting update videos, etc. I didn't have a large number of views, but the views I got were from highly specific audience. So, I get 500 to 1000 views. That's clearly something that isn't high priority to the masses of YouTube, but for the community that has built up around sharing videos like that on YouTube, it's important.