Transit agencies never have money. Any agency that ran a surplus would be highlighted as a case study in government inefficiency. They're also in a unique position vis-a-vis labor disputes. As a corporation that operates at a deficit, largely due to variable costs, a day not spent paying your workforce and not operating your passenger vehicles is a day you lose less money. A strike is more financially viable than business-as-usual.

edit: Err... Yeah, like Mr. Miskatonic said.