While local politics surely plays a role, in recent years getting money for new rail projects has required being able to show that the project will result in reduced travel time. Since reduced travel time requires some sort of grade separation, in a dense urban area this entails either subway, elevated, or massive eminent domain. All of those options are too expensive, so reduced travel time on a route requires finding a relatively non dense area with significant distance between stops. So the trains go to the burbs. That isn't necessarily bad, and I'd say it's good to the extent that land use rules around the routes change (too often they don't), but it's part of the reasons why new transit systems have a heavy suburban component.
We're moving away from that standard at DOT under LaHood, but it's how things have been.
