I googled "aircraft carrier transporting cars," and the result? The ship was moving to a new home port, where it would undergo maintenance/upgrades and the Sailors assigned to the ship would be making the new port their home. It was a 1200 mile move up the coast, so it was more cost efficient to transport that way as opposed to paying all the Sailors to make the trip on their own and reimburse them.
edit:
linky
also - there are only two other options: contract another ship to move a mass number of vehicles, or arrange for other transportation methods, usually means having the individuals arrange transport on their own and reimbursement them. This would be by far the cheapest option. Sure, it is not without risk, but the other ship method, likely still cheaper than individual arrangements, would carry the same risk.
In the event of some major disaster that would see the government having to reimburse for the vehicles, I'm sure that would be a very minor sum to tack on to the total bill for repair and cleanup in the first place.