Short answer: Because the timeline of the development of the atomic bomb ended up stretching well beyond the war in Europe, no serious planning or consideration was ever given to using it on Germany. Even the planning for how to use it against Japan did not really start until May 1945, at which point Germany was defeated.

Longer answer: There had been some discussions of possible use against Germany in 1943, and also in late 1944. Neither went anywhere serious. See further discussion and documents here.

Bonus: Would the bomb have been used against Germany had it been created in time to use against Germany? Maybe. Roosevelt seemed opened to the idea in late 1944. There would have been logistical difficulties (i.e., there were no B-29s in Europe). But it's not impossible to imagine. But it didn't work out that way. So we don't know.

Follow up: Would the USA have used the bomb during the Battle of Berlin? If so, would they have informed the USSR to give them a chance to pull out the Red Army from the city?