Freight currently makes better use of US rail infrastructure than passengers do, because freight is less time-sensitive than passengers and the geography of the US makes that a problem for rail. It does not make sense to penalize the most efficient user of a resource to benefit one of its least efficient users.
Last time I was on an Amtrak train, for a 1000 mile trip, I was delayed by 24 hours. The published timetables advertise the trip at 18.25 hours. That was a grand total of 42.25 hours. By car, the trip is 14.5 hours. By plane, 2.5 hours. A competitive bicyclist with a crew van could have beaten that train to its destination that day.
The last Amtrak trip I made before that added 4 hours to a 5 hour trip. The same trip takes 3 hours by car or 1 hour by air.
From the anecdotes gathered from someone I know who used to make Amtrak passenger rail reservations, every last timetable is complete BS. Every single passenger route not on the east coast experiences a long delay, nearly every time it makes the trip. Sometimes, the train doesn't even get there at all, and the passengers are transferred to coach buses to be dropped off in a place that may be rather distantly removed from their intended destination.
The tickets themselves are not cheap, either.
I would say it doesn't make sense to have passenger rail at all, without some tracks completely dedicated to time-sensitive passenger traffic. In that sense, the freight lines are already being penalized.
Government shouldn't optimize for "users" (esp. when it's not human) but instead it's constituency. Is the country best served by timely transport of goods (which, at-best, fares poorer to trucks) or by timely transpiration of people?
Goods. Goods don't care if they arrive in the middle of the night, or if the trip takes a (predictable) couple hours longer than driving or way longer than a flight. They also don't need to be schlepped into the center of heavily populated areas at high speeds; in fact, they'd usually prefer not to be. People do: they have better options. Trains are a good way to move goods long-distance in the US, and a bad way to move people.
Businesses care about predictable logistics; they care about throughput (and jitter), but not latency. People are different.