I assume none of us know how much income the freight trains generate, and how much that depends on "On time" pickup and delivery?
A decade ago, a BNSF manager once told me that some of the higher revenue trains will pull in $250,000 revenue (not profit/net income, just sales revenue) per departure.
I did some digging a while back (and shame on me, I keep forgetting to bookmark the links where I find this info because I’d love to go back to it and get more information) that gave sample rates of freight train revenues. I want to say that the revenue is in the neighborhood of a couple hundred dollars per car-mile. Basically, they take in a ton of revenue. I seem to recall my calculations that if a long-distance Amtrak train were to match the revenue of a freight train on a per-mile basis, it would require several hundred passengers paying higher-bucket sleeper fares.
They money they get from Amtrak in track access charges is a drop in the bucket, in comparison. Even if delays (and associated penalties) brought their Amtrak income to zero, it still wouldn’t be more painful, financially, than having to reduce freight traffic to let Amtrak through on time. This, right here, is the crux of the issue for why freight railroads don’t like Amtrak. An Amtrak train can take up more than one freight train slot (because of higher speeds, plus, sometimes, the need to accommodate a train going the “wrong way” on a long, single-track railroad when the freights could otherwise fleet their trains), yet brings them very little revenue to do so. Amtrak OTP does okay when the railroad is not full, but when freight traffic picks up to the point where they need every possible slot, OTP goes down the toilet. And it doesn’t matter how “friendly” the railroad supposedly is, either.
Remember when the Empire Builder, running on “passenger-friendly” BNSF had the best OTP of any long-distance train (early to mid 2000s)? Then, suddenly, BNSF realized that their little-used freight line in northern North Dakota (so little used that they were ready to abandon a part of it through Devil’s Lake, and Amtrak was drafting up plans for a reroute) was useful for all of the oil fracking going on in North Dakota, and almost overnight, the Builder’s OTP dropped to nearly zero. It got to the point where Amtrak had to add an extra consist to the Seattle & Portland end because otherwise trains had no chance of departing the west coast on time.
Take a freight train pulling in $250,000 on a route half the length of the Empire Builder, and then try to see what a passenger train would have to earn in fares to even come close to that, and the math becomes very difficult to pencil out in favor of the passenger train in any scenario where both share the same tracks and you are facing potential traffic that is meeting or exceeding those capacity limits.