Well that just confuses me more, if the losses are spread out across all these counties each with their own revenue, why isn't that the default place where money is allocated from?
SEPTA was formed by the state, and its existence benefits the whole state by enabling economic activity (which then leads to more state-level taxes), reducing congestion on roadways maintained by the state, etc. And if my back-of-the-envelope math is correct, nearly 1/3rd of PA's population lives in counties served by SEPTA.
When a transit agency serves the state's largest population center and economic center, it seems reasonable for its funding to be a state-level concern. Especially when it also serves other states, and additionally ~40% of the tracks used by SEPTA are owned by Amtrak, which is Federal. County-level officials are just not the best layer to interface with all that.