Talk about a buzzkill. Sybok thought he was traversing the universe to meet God, but it turns out that he was just a mark for the greatest con artist in the galaxy.
Here's the deal: at some point, Sybok received a telepathic communication from a dude he believes is God. This apparent deity asked Sybok to travel to the center of the galaxy and find him on the planet Sha Ka Ree, presumably to bask in his glory and all that jazz. Being a bit of a whack job, Sybok takes the bait hook, line, and sinker.
At first, God fulfills his expectations. He's represented by a mass of blue energy with images of various deities floating inside, symbolizing Sybok's belief in the validity of all religions. The deity finally settles on the traditional Western conception of God: an old man with white hair and a bushy beard.
Unfortunately, the honeymoon is cut short when God blasts Kirk, McCoy, and Spock with glowing energy because they dare question him. Someone needs anger management.
From there, we learn that God is, in fact, an intergalactic prisoner—and Sha Ka Ree is his prison. That certainly changes things. Putting aside the notion that this guy can communicate across the galaxy but can't escape a planet, this suggests that attempts to find the "literal" meaning behind religion are foolhardy.
In the film's closing moments, Kirk seems to back up this idea when he says that even if God doesn't exist "out there" somewhere, he exists within the human heart.