Gotfredson told ABCNews.com that he sent the warning because of "the nonsense in the papers I've been reading about barefoot running."
"It's a fad," he said. "You'd have to have such pristine conditions to make it safe."
Still, he said he doesn't take issue with the biomechanics of barefoot running.
"If you don't need support, if all you need is protection, that's fine," he said, but he added that the reality his company sees time and again is that people need support.
He said that whatever works for individuals is the appropriate way to run, and though people can change their style of running it's a "major project."
Dr. Pierre D'Hemecourt, the medical director for the Boston Athletic Association, which organizes the Boston Marathon, said he was "cautiously interested" in barefoot running.
"I think it's very interesting. I'm very pro looking at it. I think it makes some very interesting biomechanical statements," he said of the recent study in Nature. But "a lot of people running in the regular shoes are doing quite well with that."
He said that runners could ease their way into the barefoot or minimalist approach to running with shoes that have smaller heels and arches. But he emphasized that more studies are really needed to look at injury rates associated with different styles of running.
"I think I would chalk it up as a very interesting study," he said. "I think that if people were interested in testing the waters I would take very small doses at a time."