Generally, two sides have formed around the NYC mosque issue. One side says it is immoral or wrong to build a mosque so close to the 9/11 site, however, they have a legal right to do so. Another side says that it should be prevented legally, that is, the government should actively move to shut it down. I will not consider the side that actually promotes its existence. Since this argument has been beat to death in many corners of the Internet and elsewhere, I will not attempt to characterize the debate or offer new concretes. My goal is to answer a broader question related to this issue.
If the Emperor of Japan or Adolph Hitler had attempted to set up a recruitment office in the center of New York during World War II, the U.S. government would have had every right to shut it down. Whether they were motivated by Shinto or Nazism would not have made a difference, i.e., one could not have argued that the government were stifling a particular ideology since these persons were actively engaged in a physical war with America. I doubt many would argue with this presumption.
So, at what point does a "religion" or any doctrine move beyond a mere body of abstract thought, deserving protection under the First Amendment, into a philosophical or legal area wherein a proper government has objective moral and legal grounds to prevent followers from pursuing recruitment, dissemination, assembly or political organization? To me, this is the essential question underlying the New York mosque issue. In this context, the question is whether Islam is a "religion" in the sense that it is meant within the Constitution or more broadly construed under the principle of individual rights or whether it should be considered a "political movement" that is actively at war with America and/or the broader legal and cultural framework known as western civilization?
Philosophically, faith is the acceptance of an idea in the absence of evidence and is the characteristic which distinguishes religion from science. I do not believe that the concept of "faith" is relevant in a legal context, i.e., the essential epistemological foundation for a view point is not relevant. What is relevant is whether a body of thought or set of doctrines espoused by some organization can exist within a broad legal framework founded upon rational definitions of individual rights such as free speech, freedom of the press, property rights, due process, etc. Whether or not a certain ideology takes issue with applications of these principles is not important. However, if an ideology by its nature opposes the very foundation of this framework AND actively seeks to undermine this system through violent means, i.e., the initiation of physical force, such an ideology moves from the status of "religion" or "ideology" to an active enemy of civilization. Whether or not the state has formally declared war on such an ideology is not important as many instances of this type of organization could exist or spring up.
With respect to the particular mosque issue, I believe that Islam should be considered an active enemy of civilization. Although I am not an expert on Islam, from what I understand, there is very little separation between its doctrines and their manifestation in the political life of its adherents. It's followers advocate Sharia law which is a set of legal traditions that stand in complete and total opposition to western precepts of individual rights. Husbands can beat and rape their wives. Stonings and hangings are common to those who speak out against the religion or convert to another (apostasy). It is intolerant and hostile to non-believers in the most vile, racist, and violent ways imaginable. Its goal is the complete enslavement of mankind under a global caliphate, i.e., global theocracy, and it has killed tens of thousands in this effort.
Rather than be seen as a "religion of peace" with a few extremists tarnishing its essence, it should be seen as a global political and military force that seeks to spread throughout the world. If this movement were contained to other nations, I would argue as a matter of foreign policy that we have no interest in opposing it militarily. However, as this movement has repeatedly attacked western interests and made its motivations and goals crystal clear to anyone who will listen, the U.S. government should officially regard Islam as our ideological enemy and take any steps towards thwarting its spread within our borders and by supporting allied efforts to do the same.
Also, to answer the argument that only some Muslims are "extremist" I would say the following: just as every Nazi was not a Hitler or Goebbels, and not every Japanese citizen was a kamikaze during World War II, this is not relevant. What is relevant is the actions of its most consistent advocates and its leadership alongside the inaction of its so-called silent majority. It is up to them to rise up and moderate or reform their "religion" in such a way that it can co-exist with the West while broadly respecting the basic principles of individual rights. If, by its very nature, it can not exist in this way, then we should not respect the rights of its followers as they do not respect ours.