The only thing I could find of particular usefulness to this question was a local article on patch.com, which contains this blurb regarding an interview with David Milch (the series co-creator):
“The idea [behind John from Cincinnati is] that the universe is a
solid system but [also] a series of waves,” he said. “And that man is
not an individual creature, but that his essence is carried from
seeming individual to seeming individual [and becomes] available to
surfers if they aren't loaded and selfish or if they don't become
addicted to the behavior of surfing itself."
He also states that the rush for production was counter-productive and he didn't have time to fully develop the story or characters.
Additionally, this review of the show gets very indepth, and states the show is about
"forsaking the rational in favor of the unknowable. John From
Cincinnati at times feels more like a waking dream or a visual poem
than a conventional TV series."