Being a recent Michigan Alum, I can speak towards the low numbers in Ann Arbor...
First, the campus is very nicely interwoven with the city. If you live on central campus, you can easily walk to anything you need. This obviously reduces bus ridership...
Secondly, and the #1 reason in my book, is nearly all of the students use the blue Michigan buses to get around campus. These buses do not keep ridership tallies.
I did ride the AATA while living in Ann Arbor and that is because I did not live on or near campus. I was about 3 miles away from North Campus (Where my program was) and when my car wasn't functioning or I didn't want to risk the parking ticket, I would walk to the bus stop and take it in. Not sure how it is now, but a few years ago (2005) your student ID only got you free rides on a very select number of routes (mainly Park N Ride Routes) so that could have an affect on reduced ridership numbers also. (I do believe all AATA routes are free for students now)