In season four and five, Supernatural made a pointed effort to avoid putting God in their show, which I actually felt was a good decision. Many shows that incorporate the apocalypse tend to make Satan as powerful as God, which pisses me off because it is just so theologically inaccurate. However, if God is more powerful than Satan then there is no story, which is boring. Supernatural makes a point to say that God is more powerful than Satan, than anyone really, but God never appears, allowing the story to still have conflict.
This created some theological problems, because God ignores Sam, Dean, and Cas, and actively states that he doesn’t think the apocalypse is his problem. But really, those theological problems aren’t that bad, because it’s something that we all go through. Namely, why does God let bad things happen to good people? God’s reasons for not intervening could have remained mysterious and beyond human comprehension.
But then something happens, at the end of “Swan Song,” Chuck, the prophet is revealed to be God. It’s not exactly stated so fans still debate over whether or not Chuck is God, but it’s pretty much been confirmed.
But if Chuck is God, many more problems arise.