I don't know a lot about the economics of the deal but I do understand they can be misleading because of the way costs are allocated. For example in the pre-Amtrak days (anybody remember them?)) railroads were accused of inflating the cost of passenger trains by saying for example half of costs for track maintenance could be charged to passenger trains even if there was only one passenger train a day and several freights, and even if passenger trains were discontinued the railroad might still have to pay the same amount to maintain the track for high quality freight service.
Regardless of the cost to ports we've undoubtedly saved a lot of time is money for people in cars not being delayed by long slow trains blocking crossings. I'm sure air quality is a lot better because of the reduction in cars waiting at crossings and there's no way to tell how many lives were saved or extended by eliminating all the exhaust fumes because fewer people were killed by eliminating many crossings.