My guess:
The Walmart baker knew what the black and white pattern was, and freaked out, and reported the customer to the FBI, but never mentally connected the customer's request to the Confederate flag stink. The Feds, and the baker's Walmart supervisors told the baker to just "quietly give the customer what he wants so he doesnt get suspicious, but take down all the information on his driver's license so we can keep tabs on him."
So now the all American good'ol'boy publicity hound who ordered the cake is in the NSA database as a suspected Arab terrorists, and he doesn't even know it!
Or maybe I am just getting paranoid in my old age. Lol!