Even the author of that research paper that that book is based on doesn't run marathons barefoot. He said humans aren't meant to run 26.2 miles nonstop barefooted.
It is believed to be one of the oldest hunting techniques, and so would indicate that humans are in fact meant to run long distances. According to Wikepedia, the runner runs for "about two to five hours over 25 to 35 km (16 to 22 mi)".