One large problem is passenger rail is a second class citizen on US rail, legally it’s supposed to be given priority but ultimately it’s all on private rail and enforcement is non existent so it’ll get delayed for things caused by cargo. I had an Amtrak journey that had to sit and wait for an hour or two to let the tracks cool after a particularly heavy cargo train had gone by.
I would counter this by offering: Long Island Railroad, MetroNorth, New Jersey Transit, MBTA Commuter Rail, Bay Area Rapid Transit, and Caltrain. (Sorry, I don't know about the Chicago system.) All of these are very good commuter rail systems that mostly own all of their track or have primary right-of-way, so undelayed by cargo trains.
Mbta commuter rail is not a good system. I tried it for a month (Fitchburg line), the train was scheduled once an hour and was regularly half an hour or more late. The passes were exorbitantly expensive, too; more than the cost of car ownership for the same route. I so badly want it to work, I love the idea of it, but the day to day experience is comically bad.
I checked Wiki for more info about the MBTA Fitchburg line. I don't know from what station you rode, but MBTA commuter fares are much cheaper than the total cost of ownership of a car per mile. Estimates are about 81 cents per mile to drive a car (depreciation, fuel, maintenance, repairs, insurance, etc.) -- I Googled for it. Fitchburg station to North station is 53.7 miles, which would cost 43.50 USD to drive a car. The current MBTA fare is 12.25 USD -- much cheaper than owning a car.
Chicago's commuter rail system is called Metra (operating code MTX).
They own some of their own rails. UP and BNSF operate 4 of their commuter routes. CSX owns most of a few of the Metra operated routes.
Once, I was delayed 2 hours on Christmas Eve by a 1 Mile + Long freight train that broke down while crossing our main line pulling into the freight yard south of O'Hare Airport. A victim of CSX's "precision scheduled railroading".
Back when Metra pre-recorded the automated announcements, they specifically had one for delays caused by "freight train interference". The freight operators don't give a flying fuck who they interfere with, because they are empowered to.
Those are all local systems, all the cross country and intercity (for cities where their suburbs haven't merged like Chicago or the NE) stuff has to share tracks with cargo rail.
That lack of delays from cargo is also why they work a little better. One other big delay though is that basically none of the trains operate as expresses so they have loads of little stops along the way serving all the little towns along the route where little delays build up and by the end of the run they're sometimes hours behind schedule.
But commuter rail is pretty different, right? The point of discussion was more around the restrictions of intercity.