I've transported a number of them and what I usually do is take a 10 or 12" cake box and fully assemble it, including taping the lid down. I then cut a circle in the centre of the box approximately 1" smaller then the opening at the top of the vessel the cupcakes are in (so if I am using 6" pots, I cut a 5" circle). When you place the pot in the box, it will be held securely upright even if the bottom of the pot doesn't touch the bottom of the box. It's definitely sturdier if it is touching the bottom, so you may want to put something in the bottom of the box. I then put them on the passenger side floor.
I hope that makes sense!