Their main argument is that the cross isn’t part of 9/11 history. Rather, it was "created" after the fact (not hard to believe, since falling steel beams often form cross shapes) and it's an example of Christian privilege at the exclusion of symbols from all other faiths.
MORE: http://www.patheos.com/blogs/friendlyatheist/2014/03/06/today-american-atheists-will-argue-before-an-appeals-court-against-the-world-trade-center-cross-display/