Short answer, yes.
I got into this question a bit with an explainer earlier this month about Chris Jeon, the UCLA student who traveled to Libya to fight with the anti-Qaddafi rebels.
It was once possible to lose one's U.S. citizenship by fighting in another country's army against the United States -- whether Al Qaeda in the Arabian Peninsula counts as an army is another question -- but as the legal blog Opinion Juris explained on Twitter this morning, the Supreme Court has found that unconstitutional under the 14th ammendment. Ironically, the virulently anti-Semitic cleric's citizenship was protected by a case that involved a dual U.S.-Israeli citizen fighting to keep his U.S. citizenship after voting in an Israeli election.
In order to lose his citizenship, it must be shown that the U.S. citizen joined the foreign military or swore allegiance to another state "with the intention of relinquishing United States nationality" -- a very tough standard. There's no evidence that Awlaki ever formally renounced his U.S. citizenship.
A bill was introduced in the House last year by Rep. Charles Dent (R-Penn.) which would have stripped Awlaki of his citizenship on the basis that his calls for attacks against the United States constituted a voluntary relinquishment, but it never made it out of subcommittee. In any event, the Obama adminsitration never denied Awlaki's citizenship when it targeted him for assassination.