Not when they're spread out over 9 lines and an entire metropolitan area.
A little spreadsheet I put together with numbers from the 2014 Blue Book.
https://docs.google.com/spreadsheets/d/1_5A9ziNUWsgfnhRXT5e_634kFgGOgfzSh0rEaPw18o8/edit?usp=sharing
Several lines average close to 200 passengers per train on Saturday. Seems like pretty healthy ridership to me. Despite the pathetic weekend schedules, the trains are being used.
Of course any commuter rail ridership figures should be taken with a grain of salt.
http://commonwealthmagazine.org/transportation/commuter-rail-ridership-numbers-dont-add-up/