I haven't had a chance to test this, but you can try setting a checkpoint somewhere "legit" like the road and then hovering over it and pressing the button to Edit the checkpoint, and then move it into the airport. Also, are you sure you're placing the checkpoint and not the trigger for the race? I could definitely see it considering the airport as off-limits for triggers, and probably even checkpoints as there is always the chance to have flight traffic moving through the area.
Side note: you're probably aware, but R* probably doesn't use the same Creator (Beta) that you and I use, so they can pretty much do whatever they want. Notice that we can't put checkpoints under long underpasses, as the camera won't fit, but they do it fine. I would bring this issue to their attention, as the Creator is in Beta and will hopefully continue to get revisions improving the capabilities of regular users.