Contrary to many critics' opinions, I do not believe the whole Dr. T.J. Eckleburg thing is a symbol, and it has nothing to do with God.
It is an old billboard for an out of practice oculist. It is faded, and this, along with the entirety of the "valley of ashes," gives the impression of dreams lost. A man opened a practice...it was his dream. Now that dream is over.
Also, much of this book is about characters projecting illusions of meaning onto things and people where it does not exist. If anything, Nick's description of this billboard might give off a feeling of a being looking down upon the valley, but he's just doing the same thing he does with Gatsby: thinking it's greater than it is.
As for God, Wilson only says he sees God in the billboard, one he's likely to have seen many times in his life, after he finds his dead wife. In times of great distress we sometimes suddenly see God, where he does not exist. This is not unlike Gatsby seeing the green light as something to reach for, when, in the end, what he thought was near it turned out to be a pipe dream.
In other words, the billboard is just a billboard, the green light is just a green light, and The Great Gatsby is just a guy named James Gatz. Oh, not to mention, The Great Gatsby is another illusion. We get wrapped up in it, but in the end, it's just a bunch of ink on paper, and when we're done with it, we're left with nothing but ourselves.
Or so I think.
Moreover, the eyes also symbolize the corruption of America’s people. The eyes of Dr. T.J. Eckleburg stare down on the main characters as they pass underneath the billboard on their way into New York City where Tom carries on his adulterous affair, where Gatsby drives Nick to meet Wolfshiem, the man who fixed the World Series, where Daisy rushes off to find a few thrills with her over, Gatsby. The eyes seem to frown down on these characters, Wilson equates T.J.’s eyes to the eyes of God. He recounts to Michaelis what he says to Myrtle after discovering his affair, “‘and I said “God knows what you’ve been doing, everything you’ve been doing. You may fool me, but you can’t fool God!”” However, Michaelis tries to point out to him that “It’s just a billboard.”