Doing so forgets the human side of the equation. There is technically a couple ways to avoid the fee (eg: self-certifying as a bicyclist, walk to work or carpoo

Doing so forgets the human side of the equation. There is technically a couple ways to avoid the fee (eg: self-certifying as a bicyclist, walk to work or carpooler) which give the city fairly accurate data as to how people get to work. Meanwhile, employees feel better about their emploer giving them a "free" transit pass rather than a tax funded passes for all plan. It creates a surprisingly strong incentice for people to switch companies to one that will give them a transit pass (particularly among the $100+k a year workers). Employees literally feel jipped when their employer doesn't give them a pass, I don't think you could create this kind of positive incentive to be a transit rider any other way.