It is a private bus operator, who does not receive one red cent from the city or any government agency. In fact, they PAY the city $22,000 a year for driving the route. A private bus has a constitutional right to adhere to their religious leaders religious beliefs.
Also, the passengers enforce the seperation, not the driver or bus company. The driver has no obligation to involve himself in conversation or interactions between passengers. In fact it would be dangerous for him to do so while driving.