I use the R line a bit more than I would if I had to pay each time. I really notice the time saved when people can just get on. Most importantly, the service is almost pretty damn good.

If there is a choice between great service at affordable cost or crappy free service, most people would rather pay. (edit: getting to work consistently on time can matter even more when you do not have a lot of money)

I think an honor system for payment would lose less $ to fare evaders than it would save in collection related expenses. That crappy app is going to have be patched and updated forever. Better to pay drivers than coders. If the service is good, all but very few people who can truly afford to pay will pony up.