Hadn't seen this before but it's interesting, their 'number of weekday riders' section is similar to the way we displayed station entrances over time. Thanks for the link!
There are lots of influences from Tufte, the image you link was one of them for sure. We tried to incorporate other ideas like fully integrated text, numbers, and graphics and showing comparisons and causality. Bret Victor's work was also a big influence. If you are interested in what the design and implementation looks like and are in the Boston area there's a meet up this Thursday where we talk about building this:
http://www.meetup.com/Data-Visualization-in-MetroWest-Boston...
Most of the data is collected from the MBTA's real time data feeds that list the current positions of all of the trains. The capacity data (who's entering and exiting the stations) is collected at the turnstiles and is not part of the MBTA's public API, we were able to get this from the MBTA through their developer relations program http://www.mbta.com/rider_tools/developers/.