The issue is not of having a cross on publicly funded locations. It's that once you do that, you must provide equal opportunity to all.<quoted text>
I missed the part of the story where they were building a publicly funded church in the 911 museum. Of course, there are quite a few publicly funded places of worship in the US -- at least one on every major military post. Many in public hospitals. Others are just historical sites that receive public renovation funds (the Old North Church in Massachusetts for example).
American battlefields like Pearl Harbour and Gettysburg receive public funding and have crosses on them. I don't think it's too much of a stretch to call the site of the WTC an American battlefield.
Public "chapels" are intended for multi-denominational use (including secular use by atheists/humanists), so no preference being shown there. Thus, not an issue.