Given the history of nations that believe God to be on their side in all things, it is helpful to realize that God holds no citizenship–a lesson Abraham Lincoln evidently understood.
Ministers and theologians, who day and night studied the Scriptures, knew very well where God stood on the war (though, of course, they differed among themselves). We would expect Lincoln, as the Union’s president, to be just as partisan as Beecher. We would assume Lincoln to be just as vituperative about Southern leaders as Dabney was about the North’s. Yet Lincoln, though he pondered the ways of God almost as steadily as the professionals of religion, was not so sure.
Admittedly, in his first inaugural address, in March 1861, Lincoln had presented a fairly conventional view of God and the American nation. The “ultimate justice of the people,” he said, would prevail, for there was no “better, or equal, hope in the world.” Lincoln saw a solution to the national crisis in terms of civil religion: “Intelligence, patriotism, Christianity, and a firm reliance on Him, who has never yet forsaken this favored land, are still competent to adjust, in the best way, all our present difficulty.” God, in other words, would stick with the Americans, whose own virtues would lead them out of trouble.
Soon, however, the vicious realities of war began to stir something else in the Northern president. As early as 1862 Lincoln began to think the unthinkable: Perhaps the will of God could not simply be identified with American ideals and the effort to preserve the Union.
via The Puzzling Faith of Abraham Lincoln | Christian History.