Doesn't really change the facts. American Atheists are not arguing that they should use Atheist symbols. The article you used just says "some atheists" are making that argument, with no citation, examples, or any sort of fact behind that.
Honestly I can say I would enjoy if other religious symbols were there. Not to represent the religions, per-say, but to represent that it was the World Trade Center. All kinds of people from all over with totally different beliefs died that day.