Sgt Pepper had it right, you are mistaken. Any military plane that the president is on board automatically becomes airforce one. He could have hopped on a C-130 delivering supplies to troops stationed in Iceland, but the moment he steps on that plane it becomes air force one. Both of the official "air force one" planes that have the fancy paint jobs are real and fully functional (there is no decoy), so the president could have easily flown anywhere if he needed to.
If he didn't fly today, it's not because he wasn't allowed to, it's because he had no reason to fly.