Well, that's just it. Ideally, we'd find ways to bring down all costs without cutting service. For that matter, it would be great to have a more integrated system (OMNY's a step, but it's far from the only necessary thing). And yes, if we need to reduce the ferry subsidy (if I'm being honest, a $6.75 fare is too much if the plan is to transport more than the wealthy) to put more money into other transit modes, then so be it.
The reason I take issue with the express buses in particular is because those routes physically have the fewest restrictions and use the same medium as the local buses and subway, yet they're still well out of reach for much of the population simply because the inherent costs of operation negatively impact the price. (A neighborhood such as Brownsville could probably benefit from express bus service to the point of helping to lift the neighborhood out of poverty if planned correctly, but because of how damn expensive it is, it simply wouldn't make sense to run one through there.)