The professor is correct. During the show for which he was fired he did not call the terrorists freedom fighters.
I have highlighted the statement in question that got him fired, made 6 days after 9/11 on his talk show "Politically Incorrect".
Draw your own conclusions. Maher has stated he was not referring to the military, who actually fire those missles he mentioned, but to the collective "we", as in US citizens. Keep in mind the WTC were still smoldering on 9/17.
On Monday, September 17th, Maher and his guests were discussing the attack on the World Trade Center -- primarily, what could be done to prevent further attacks.
Part of this discussion included the following exchange between Maher and conservative writer/commentator Dinesh D'Souza:
Dinesh: Bill, there's another piece of political correctness I want to mention. And, although I think Bush has been doing a great job, one of the themes we hear constantly is that the people who did this are cowards.
Bill: Not true.
Dinesh: Not true. Look at what they did. First of all, you have a whole bunch of guys who are willing to give their life. None of 'em backed out. All of them slammed themselves into pieces of concrete.
Dinesh: These are warriors. And we have to realize that the principles of our way of life are in conflict with people in the world. And so -- I mean, I'm all for understanding the sociological causes of this, but we should not blame the victim. Americans shouldn't blame themselves because other people want to bomb them.
"Bill: But also, we should -- we have been the cowards lobbing cruise missiles from 2,000 miles away. That's cowardly. Staying in the airplane when it hits the building, say what you want about it, it's not cowardly. You're right"