The Transport Politic has an essay up that argues:
He uses various regions as exemplars. This is a complicated topic for transportation because regional agencies, he’s right, get whipsawed between competing constituency demands. However, cities do, too.
The reasons these types of regional institutions emerge is that regions simply grow; employment and commuter sheds grow to encompass multiple jurisdictions, and as charitable as it would be for central city transit companies to serve extra-jurisdictional residential and job sites, they just can’t do it. So regional service is necessity for resource sharing and planning and for creating the sort of quality transit services are are actually useful to commuters: look at the massive area that the New York MTA now serves. But as, TP notes, all that is a lot easier said than done.
Also throwing a spanner in the regional works is the bottom line that it is easier to coordinate services across one regional institution…but there are diseconomies of scale in transit service as well, and these can be pretty bad.