It also costs nine cents to mint a nickle. The justification behind a coin costing more than it's face value is that since it would be used more than once, it is still worth manufacturing.
It also depends on the raw material's price at the time of fabrication. In 1981, Reagan's administration proposed making the penny from zinc. The Copper and Brass Fabricators' Council sued, saying the plan would shackle the U.S. government to the whims of capricious foreign zinc miners, since much of the zinc used in the U.S. comes from Canada. Because of the lobbying and other obstacles, it took the government two years to fully introduce the copper-plated, one-cent zinc piece, which managed to lower the price of the penny fabrication.