This organization, part of the Department of Transportation, generates a variety of statistics on the U.S.'s transportation system. Besides "Transportation Statistics Annual Report," this site includes extensive data (in spreadsheet format) from "National Transportation Statistics." In addition, they have the "FAA Statistical Handbook of Aviation" and the "Commodity Flow Survey," a joint project of the DOT and Census which tracks shipments in the U.S.
http://www.bts.gov