Hardened Containers for Air Cargo Security Act of 2004 - Directs the Secretary of Homeland Security, acting through the Administrator of the Transportation Security Administration, to: (1) carry out a pilot program to evaluate the use of hardened containers for cargo and luggage on passenger aircraft to minimize the potential effects of an explosive device; (2) develop guidelines for use by air carriers in determining the types of cargo and luggage to be placed in a hardened container on a passenger aircraft; and (3) carry out an incentive program to provide assistance to air carriers to test the use of hardened containers for cargo and luggage on passenger aircraft. Requires an air carrier to apply to be eligible to participate. Includes among assistance provided by the Secretary both the use of hardened containers and financial assistance to cover increased costs to the carriers associated with use and maintenance of the containers, including increased fuel costs.