Many Atheists and Agnostics believe that if God did exist, he wouldn't actually play an active role in human affairs. There is something to say for that viewpoint, considering the lack of fate or control present in our day-to-day lives, and how feasibly a morally good, benevolent person wouldn't just sit and watch while the people he/she cares about suffer. Or one could argue that God doesn't intervene with humanity because it believes that free will is more important for the human race. Given Alan Moore's spirituality, he may believe in spiritual forces in our world, but it's highly unlikely that he belives in an authoritarian God that actively controls what we say and do. And his portrayal of Dr. Manhattan doesn't dispute this.
This view is best demonstrated in Chapter 2, where Dr. Manhattan just watches while The Comedian guns down his pregnant Vietnamese girlfriend. The Comedian tells Dr. Manhattan that if he really wanted to save that woman and her baby, then he could have "turned the bullets into mercury, turned the gun into snowflakes or teleported either of them to goddamn Australia". But he didn't, because he no longer cared about the suffering of humanity.
Basically Dr. Manhattan represented God, and The Comedian gunning down his pregnant girlfriend represented the suffering of humanity.