They did it for a mundane reason
Anyone accepting the government payout has to waive suing the airlines or presumably the government for responsibility for 9/11. Now, under the laws and Federal Aviation Regulations in effect on that day, the airlines and airport security people did nothing wrong but that means nothing to sleazy lawyers looking to cash in on a class action suit. The airlines have many friends in Congress, including Tom Daschel whose wife is a lobbyist for at least two airlines.