As Kvatch pointed out at Blognonymous, the reason it's bad that John Gilmore basically lost his suit against the TSA for requiring photo ID before flying is not so much that people should be free to travel on airplanes without identifying themselves. It was more about requiring government agencies to make known what the laws and regulations are that citizens have to follow, and give citizens a chance to review and challenge such laws and regulations.
In effect, when the Supreme Court refused to hear the case thus upholding a lower court ruling against Gilmore, they gave the green light to the government to just make up rules and laws as it goes. Like the Bush Administration has been doing for six years now.
This doesn't bode well for the Supreme Court's decision concerning the case against the Bush Administration directing the Secret Service to refuse to release the White House's visitor logs by arbitrarily reclassifying them as "presidential papers" to hide Bush's connections with Jack Abramoff.