As a uniformed government employee, I do have to say that if a dress code is in place, you have to abide by it.
BUT looking at some of my fellow employees, whose dress code is "business casual," a kilt would be a definite improvement.

If you're determined to address this issue, there are a few threads here you can check - search for "kilted" and "work." Confirm, if you can, that the no-kilt rule is a local policy (if it's national, you're sol). Find out which airports allow kilt-wearing, and what those ATCs did to get it allowed. Once you have all your facts together, present your case to your supervisor. After that ... well, I don't know how things work at the FAA, so you're on your own.

Just a thought - it occurred to me, after re-reading your post (you "decided" to wear your kilt to work) - did you ever wear your kilt to work prior to the new dress code, or was the first time after the dress code went into effect? If it was the latter, your supervisor may have seen your kilt not as acceptable business casual, but instead as you mocking the new guidelines. Something to consider.