I live close to the Natchez Trace Parkway. I understand that the route was originally a forest trail for herds of bison, then indigenous people, then settlers. Considering that, I'd like to learn more about the origins of our transportation routes from sea-to-sea. Are there any documents or books covering this in a comprehensive way?
Origins of non-interstate roads are pretty easy. A lot are laid over Indian trails, like Broadway in Manhattan and Lancaster Pike in Pennsylvania. Here's a good website for that.
As for interstates, they were usually determined by city planners and FHWA planners. Here's a FHWA article about that.
Interstates are chosen route numbers by which direction they go, and how far west/east they are to the next highway parallel to them. For example, there's I-95 and I-75, I-20 and I-30, I-91 and I-93, and I-94 & I-96.
Other non-interstate roads that were former Indian trails include Natchez Trace, Blue Ridge Parkway, and Route 220 in Maine. Here's an article about historic Indian trails in New England.