Airlines have long criticised the September 11 security fee so it's understandable why they're so upset about this latest hike

The Sept. 11 charge on airline tickets is often referred to as the TSA fee since the money supports airport security. As of July 21, it rose from a low of $2.50 to a flat $5.60 one-way. It is not an optional fee and is embedded in the price of your ticket. Airlines collect it and disburse it to the government.

Because the fee is embedded in the cost of your ticket, to the flying public it looks like yet another fare increase or fee addition, so the airlines bear the misguided rage of passengers who feel like they're constantly being nickled and dimed. 

Further to that, airlines will have to retool their reservation systems to accommodate the new fee structure, which costs time and money.