The rail system predates the interstate highway system by almost a century. The reality is that the highway system was built by the government, and the rail system was built by private companies. The government had better planning tools than the private companies (eminent domain), and ended up with a better system.
Furthermore, if you look at old maps of many cities, you'll note that many current highways either are adjacent to still-used railroad tracks or use the right of ways of railroad lines that no longer exist.
