Like the Wizard of Oz, the dude found at Sha Ka Ree is revealed at the end of the movie to be a complete fraud. At least there's a blissful absence of flying monkeys in this one.
What our heroes learn when they get to Sha Ka Ree is that from the start, everything has been a giant con. God didn't contact Sybok in order to spread his knowledge throughout the galaxy; he was tricking him into breaking him out of his interstellar prison. And everyone would have bought into this lie if it wasn't for that meddling Captain Kirk:
KIRK: What does God need with a starship?
MCCOY: Jim, what are you doing?
KIRK: I'm asking a question.
GOD: Who is this creature?
KIRK: Who am I? Don't you know? Aren't you God?
God responds to these questions with multiple blasts of energy—he has nothing to say, so instead he just makes a big show to distract everyone. These actions immediately turn the crew against him: even if he is the Big Guy, our heroes don't have any respect for his reliance on fire and brimstone.
And then, of course, they learn of his dastardly deception.
Ultimately, the film suggests that it's perhaps impossible to find the "truth" behind religion, however you might define that. Instead, it seems that the subjective, personal nature of spirituality is more important than establishing its literal reality.