The report says "None of those fees should be charged, the task force said, until repairs are made to the public transit system." so it wouldn't be like they'd be "surge charging" a necessity like schools.
So, the city would not be surge charging for a necessity, just a preference for a high demand school. Likewise, most people would prefer to drive if they could, but the physical limitations of the system require that most people take public transport.
Sometimes this is also a preference for safety, as I learned attending k-12 in NYC. And sometimes the safety isnt a result of bad students, but a result of the entire system just allocating more resources to some schools over others.