Comment by OgsyedIE

Some of them date back to 'westward expansion', where they were incentives to encourage settler immigration (e.g. Texas tax exemption from 1839). They've stayed on the books because nobody wants the trouble of suggesting their removal.

More generally, however, it's a cost that is paid to support massive efficiency gains in other sectors. Like roads, aviation or the military. The freight system particularly would be unreliable if food prices floated according to only supply and demand, due to freights vulnerability to political upheavals, militias, etc.