The security fee, which pays for the ever more stringent procedures required in the aftermath of September 11th, is actually an airfare tax, not a cruise tax. According to the Federal Aviation Administration, “the fee, commonly known as the "September 11th Security Fee," will pay the costs of providing Federal civil aviation security services at U.S. airports. This is effective for air tickets issued on or after February 1, 2002. Air passengers will not be charged more than $10 per round trip or $5 for one way flights for this fee.
Bottom line: anybody who flies to or from their port of embarkation (or debarkation) is going to pay it but the fee will be most obvious to those who buy their airline ticket from their cruise line.