Ever since the 9/11 terrorist attacks, airport security has become tighter. That means x-raying carry-on luggage before allowing passengers to take them to the airplane. Unfortunately, some carry-on luggage can include pet carriers.
So airport security officials are warning passengers not to put their pet carriers, with their pets, in the airport security x-ray machines. The proper method is to remove your pet (if possible) and let security officials x-ray the pet carrier. Then put your pet back in the carrier afterwards. This will keep everyone happy, especially your cat.