It is the ultimate Yes, But.
First of all, here is what Dr. Chomsky actually thinks of the level of intellectual shallowness required to be duped by 9/11 denialism.
So right away, we know this claim is rather fishy. What did Chomsky actually say, that this website used to essentially lie about Chomsky's stance on 9/11? They quote this PressTV interview write-up.
“The explicit and declared motive of the [Afghanistan] war was to compel the Taliban to turn over to the United States, the people who they accused of having been involved in World Trade Center and Pentagon terrorist acts. The Taliban…they requested evidence…and the Bush administration refused to provide any,” the 81-year-old senior academic made the remarks on Press TV’s program a Simple Question.
“We later discovered one of the reasons why they did not bring evidence: they did not have any.”
The political analyst also said that nonexistence of such evidence was confirmed by FBI eight months later.
“The head of FBI, after the most intense international investigation in history, informed the press that the FBI believed that the plot may have been hatched in Afghanistan, but was probably implemented in the United Arab Emirates and Germany.”
Chomsky added that three weeks into the war, “a British officer announced that the US and Britain would continue bombing, until the people of Afghanistan overthrew the Taliban… That was later turned into the official justification for the war.”
“All of this was totally illegal. It was more, criminal,” Chomsky said.
Ah, so his view of the evidence is that the attacks were "implemented" in countries other than Afghanistan, rendering the Afghanistan invasion illegal. That's a question of geographic location, not organization responsible. Worldfor911Truth lies to its readers - it's up to them to decide what to do about that fact.