We shouldn't assume that more income from congestion fees will be used for transit improvements. First of all, you can expect the unions to see the increased city coffers and demand pay increases. Secondly, you'll have existing programs that have been underfunded now getting a funding boost, such as the TCHC, shelters and existing infrastructure.
By the time the congestion fees make their way to the city's general revenue account, they'll be little left for transit....unless....the mayor himself, like London's mayor, forces the funding toward transit.