Actually, highways are probably the least subsidized mode of transportation due to the fact that most federal highway funding comes from fuel taxes. You can make an arguement that autos pay a disporportionately higher percentage than truckers in terms of attributable road damage, but nonetheless main roads are mostly self supporting.

The barge lines are "subsidized" in as much as slackwater barges can carry more cargo than the old steamwheelers of the free flowing river era, but in theory it is the output of the dams that support the lock and navigation channel costs. If you believe the dams have paid for themselves over the years via low cost electricity production, then it can be argued that the general taxpayers have not subsidized the barge lines, rather the cost of lock and navigation construction/maintenance is really just a part of the larger cost of dam construction/maintenance. If the dams have paid for themselves many times over, then there is no actual barge line subsidy coming out of the pockets of the taxpayers. If however you feel that Northwest electric rates are unnaturally low compared to other parts of the nation due to the way federal dams are operated then of course that would include the navigation system.

The railroads (at least in this area) by and large benefitted from the land grants. The NP land grants were so massive that when Hill took over the NP it may very well have been the NP land grants that kept the GN from bankruptcy during the Great Depression, e.g. it was the collateral that kept the banks lending. Of course Hill was willing to let the NP falter, but his baby the GN was kept out of the red.

The railroads also have the benefit of owning an unregulated natural monopoly which is not possible with barges and trucks. One can argue that lack of regulation or forced competition over natural monopolies is a form of subsidy per federal antitrust statute.

Frankly it is tiring to continue to hear this anachronistic "rail vs barge vs truck" debate continue unabated in this era of multimodalism. I would rather see modally integrated companies (rail/barge/truck of Company A vs rail/truck/barge of Company B vs rail/truck/barge of Company C etc.) competing with each other rather than seeing specific modes competing with each other. In some ways UPS and FedEx are modally integrated transportation companies, although they have to rent access to rail (and barge?) rather than owning their own rail like they do trucks and planes.