Hi Alex. The problem turned out to be a bug in the script where it was unnecessarily trying to convert the stop_id to a string, and for your particular data, it was throwing that Unicode decode error because it was trying to convert the string to ASCII.
I have fixed the problem. You can download a fresh version of the toolbox here: http://arcg.is/0yr9fr
Or, you can just download this one file and replace your local copy with the downloaded version: public-transit-tools/BBB_CountTripsAtStops.py at master · Esri/public-transit-tools · GitHub
In case anyone is reading this thread in the future, Alex's problem was unrelated to the original question posted here, even though they had similar error messages.