Indeed, bike (er, well, "cycle") compatible busses can be far between. But until this recent period where being packed in with others became an acute concern, the Metro North commuter trains (and to a lesser but still important extent, the Hartford Line and NJ Transit trains) are what made my distance riding career *possible*. One way rides to Brewster. Century attempts that became train returns from Brewster. Succesfull Centuries that left down the hill from Bryn Mawr to Bronxville and a train home. Trains to Poughkeepsie for the Duchess. Trains to and from New Brunswick, Bound Brook, Princeton Junction for the D&R and Trenton for the D&L. Then MNR to New Haven for the Farmington Canal and via the Hartford line for a day ride with the guys or to do a Century from the north end with the aid of some family shuttling.
The solitary time in all of this that I used a bus was Bolt service from NYC to Philly to ride the Schuykill. It worked, but my legs weren't happy in a small bus seat after doing a metric. Fortunately it was dark enough people didn't really notice me stretching them into the aisle.