Transit subsidies are actually what the generated toll money is supposed to be used for. The point of congestion pricing is to induce a portion of the population to switch transportation modes by making public transit a more attractive option in terms of price and quality. When London implemented the its congestion charge, there were transit improvements in place on day one: http://en.wikipedia.org/wiki/London_congestion_charge#Public...

In the US, the toll money often goes toward expensive, politically-motivated capital improvements, not operation expenses. In the worse case scenario, the money is used to build more toll lanes, which isn't going to encourage mode shift.