It is painful for me to read my old friend Christopher Caldwell's screed against the Cordoba Initiative, a complex two blocks from Ground Zero which will include a mosque within it. Essentially, Chris believes that Islam is an exception to the First Amendment's protection of religious faith. Here's his argument:
Including Islam within the fold of traditional western religious tolerance is not business-as-usual. It is an experiment. Our Lockean ideas of religious tolerance had their origins in the 16th century (the peace of Augsburg) and the 17th (the peace of Westphalia). Those understandings regulated relations between Christian sects and were steadily liberalised. Judaism later proved assimilable into this system in the US, but not, to put it mildly, everywhere in the west.
Islam which is, like Christianity but unlike contemporary Judaism, an evangelising and expansionist religion is a bigger challenge. A radical school of it views the US as its main enemy. Because that school is amply funded by Arabian oil, there is a standing fear that radicals will capture any large international project involving Islam, no matter how good its original intentions.
Notice, as Andrew Sprung does, the guilt by association. Regardless of the nature of a particular mosque, even the most peaceful, mainstream and American Muslim community is now an inherent potential terror threat. There is a "fear" that any mosque could be coopted by Wahhabist money. Therefore, no mosques are safe.
This, of course, is exactly the argument that was made about Catholicism in England (and by Locke in his famous Letter!) in the sixteen and seventeenth centuries - particularly after the Gunpowder Plot (England's foiled 9/11 of 1605). The argument was that because Catholics owed obedience to a foreign ruler, the Pope, they were not so much a religion as a cult allied to a foreign force. For the Vatican, read the House of Saud.