I don't think Falwell made that comment. If memory serves me correctly, it was Pat Robertson who made a statement to the effect that 9/11 was God's judgement on the United States because of its iniquity, including the increased acceptance of LGBT persons in some parts of the country.
That said, it is true that Falwell's interpretation of Christianity did not leave any room for acceptance of gays and lesbians within the institutional church.
Just because I was sure it was Falwell, I did some digging on the net and this is what I've found:
"Falwell apologizes to gays, feminists, lesbians
September 14, 2001 Posted: 2:55 AM EDT (0655 GMT)
LYNCHBURG, Virginia (CNN) -- The Rev. Jerry Falwell said late Thursday he did not mean to blame feminists, gays or lesbians for bringing on the terrorist attacks in New York and Washington this week, in remarks on a television program earlier in the day.
On the broadcast of the Christian television program "The 700 Club," Falwell made the following statement:
"I really believe that the pagans, and the abortionists, and the feminists, and the gays and the lesbians who are actively trying to make that an alternative lifestyle, the ACLU, People For the American Way, all of them who have tried to secularize America. I point the finger in their face and say 'you helped this happen.'"
Falwell, pastor of the 22,000-member Thomas Road Baptist Church, viewed the attacks as God's judgment on America for "throwing God out of the public square, out of the schools. The abortionists have got to bear some burden for this because God will not be mocked."
You can see the whole article here:
http://archives.cnn.com/2001/US/09/14/Falwell.apology/