Though I spent 24 years working for the State Department as a Consular Officer, charged in part with the issuance and (very rarely) revocation of U.S. passports, there is still room to learn something new: The Government of the United States can, and apparently does, take away passports from American Citizens because "The Secretary of State determines that the applicant's activities abroad are causing or are likely to cause serious damage to the national security or the foreign policy of the United States."
If the government feels it is against its interest for you to have a passport and thus the freedom to travel, to depart the United States if you wish to, it will just take it away. The law allows them to do this prospectively, the "or are likely to cause..." part of the law, meaning you don't need to have done anything. The government just needs to decide that you might.
Al-Awlaki
We learned via a Judicial Watch Freedom of Information Act request that prior to having him and his 16 year old son away blown away via drone in 2011, Secretary of State Hillary Clinton secretly revoked the passport of Anwar al-Awlaki, al Qaeda propagandist and U.S. Citizen. The State Department even tried to invite al-Awlaki into the U.S. Embassy in Yemen so they could hand him a letter announcing the revocation and so that they could encourage him to return to the U.S. to face charges. Six months later (al-Awlaki never dropped by the Embassy, by the way), the U.S. Government simply killed him. Two weeks after that it killed his 16 year old son.
Phillip Agee
I have been unable to track down many recent examples where the U.S. Government revoked the passport of an American simply because his/her presence abroad bothered-- or might bother-- the Secretary of State. In fact, the only example I was able to locate was that of infamous ex-CIA officer Phillip Agee, who in the 1970's exposed CIA officers identities. It was Agee's case that prompted a Supreme Court review of the Department of State's ability to revoke passports simply because the government didn't want you to travel abroad (the Supreme's upheld the government's ability to do so based on a 1926 law after lower courts said no. The Court stated that "The right to hold a passport is subordinate to national security and foreign policy considerations.")
Agee was a naughty boy. According to the Supreme Court:
In 1974, Agee called a press conference in London to announce his "campaign to fight the United States CIA wherever it is operating. He declared his intent "to expose CIA officers and agents and to take the measures necessary to drive them out of the countries where they are operating." Since 1974, Agee has, by his own assertion, devoted consistent effort to that program, and he has traveled extensively in other countries in order to carry it out. To identify CIA personnel in a particular country, Agee goes to the target country and consults sources in local diplomatic circles whom he knows from his prior service in the United States Government. He recruits collaborators and trains them in clandestine techniques designed to expose the "cover" of CIA employees and sources. Agee and his collaborators have repeatedly and publicly identified individuals and organizations located in foreign countries as undercover CIA agents, employees, or sources. The record reveals that the identifications divulge classified information, violate Agee's express contract not to make any public statements about Agency matters without prior clearance by the Agency, have prejudiced the ability of the United States to obtain intelligence, and have been followed by episodes of violence against the persons and organizations identified.
We Will Never Know
In Anwar Al-Awlaki's case, the Government has not made much of a case (never mind for the passport, remember he was murdered by a drone). In fact, officially, we do not know why al-Awlaki was killed at all, or under what laws or by what decision process. Some reports tie him to the failed idiot underwear bomber, but being part of a failed plot seems not to rise to the usual standard for capital punishment. It is all secret.
The Government of the United States executed one of its own citizens abroad without any form of due process. This is generally seen as a no-no as far as the Bill of Rights goes. The silly old Fifth Amendment to the Constitution guarantees "no person shall be deprived of life without due process of law" and includes no exceptions for war, terrorism, or being a really bad human being.
Could the passport revocation have been simply a ruse, a bureaucratic CYA attempt at providing some sort of illusion of "due process?" Could al-Awlaki's not dropping by the U.S. Embassy to chat about his passport have been a veiled attempt to justify his killing in that he was thus not able to be arrested? Or was the passport revocation just a simple act of dehumanizing someone to make killing him that much more palatable?
We'll never know.