If you look at the service area on the ubernyc page, it goes way beyond the city limits (even a fixed price to the hamptons). Again, even if the percentage of these rides are low, it isn't hard to see how average trip length or average fare would be moved up significantly.
I read the article - even though it's written well, it makes a lot of hypotheticals based on hazy assumptions that seem to lead well to a result that the author probably wanted to put forward. Not the best article if you want an objective analysis on the issue.