The author does discuss surge pricing.
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.
https://docs.google.com/spreadsheets/d/1N4NiwuPLo78w9PaoqXRa...
I think I mostly find it incorrect to essentially take a pin-hole view at the data through 5-6 averages, and extrapolate it towards a somewhat biased result.
As for the other data they describe their collection methodologies, and the numbers they produce are in line with trends that Uber has indicated. You're certainly free to produce a dataset of your own but until you do that this one doesn't seem especially bad or anything.