Aye, that is the historical progression: We built roads and highways for automobiles, and the logistics companies took advantage of the subsidized "free" ways. We should absolutely make them pay for what they use. It may seem like this system is "good for the economy," but this kind of subsidy distorts the supply/demand equilibrium and creates deadweight loss. Furthermore, the effect it's had on logistics favors just-in-time inventory systems, distant manufacturers, and large, centralized distribution centers. Wal-Mart and Amazon are one visible result.

Perhaps if we priced the cost of transport into the price of goods, it would be better for most people, as manufacturing and distribution (with the associated jobs) moved back closer to the consumers?