Cars take up a lot of space. A commuter rail system with a significant driving ridership, as in they drive to the stations and park for the day then take the rain, is going to needmassive amounts of parking. If you have massive amounts of parking around stations, you limit the possibility for people to actually live near and walk to the station.
There's no quick shift out of this basic model, but the emphasis really should be on transit oriented development around stations, and creating walkable communities near stations, so that not driving is an option for more people.