The lesson is this: the Law of Supply and Demand is not interested in your rationalizations or ad-hoc reasoning about "fair" pricing. In this case, the cost of living for BART employees has nothing to do with what BART should pay the employees, unless those costs cause enough employees and potential employees to quit and reduce the supply of labor.
For those of us in tech, the lesson again is that pricing has nothing to do with your costs in making a good or service. If the return is insufficient, you may either choose not to make the good in the first place, or cease making the good. It has no effect on pricing.