I think all of the suburban commuter (Metra, which is an entirely different system & agency) use freight lines, with stations typically near the town/village/city center. Problem with the shared lines is that freight (because they own the line) generally has priority. Freight train breaks down? Youre stuck for hours. 1.5 mile coal train coming through at the switch? You're stuck until it passes.
Granted, when I had to commute into the Loop in Chicago, the hour total of using Metra was far more convenient, less frustrating and cheaper than driving. It was a hour door to door for me, 15 mins to get to the station, 5 minutes of waiting, 25 mins on the train and about a 15 min walk to the office.
Now I both live and work in the West suburbs. Usually a 15 minute drive into work, about 25 home.
And that's often the problem with public transit that is built nowadays in North America (if any is built at all..) -- it's often built to outer low-density suburbs, along or on highways, with giant park'n'rides instead of neighborhoods at stations.
And that's why walkable neighborhoods with good transit connections are so rare and thus so expensive.