President Obama has weighed in the Ground Zero Mosque. If you believe in freedom of religion, you’re for the mosque. If you’re against the mosque, you’re obviously against one of America’s founding principles, the right to worship your own God, in your own way.

But that’s not the argument. The Ground Zero mosque controversy is not only about the First amendment or in which direction you face when you pray to God. People can have doubts about the mosque, and even oppose the mosque, and still be ardent supporters of religious freedom.

To some, especially those who lost friends and loves on September 11, the wounds are still so raw that they can’t tolerate anything near the site. They have never recovered the bodies of their children or wives or husbands. They were never able to bury them. The closest thing they had to the remains of their loved ones was the acrid dust that hung over Manhattan for days after September 11. For them, Ground Zero is the only cemetery they will ever have. Putting a shopping center up near there would be a sacrilege. Putting a mosque near there would be an abomination.

But, setting even setting aside objections based on what President Obama calls "emotional reasons," there are practical security reasons to question the wisdom of a mosque at near Ground Zero.

First, might it become a recruitment station for terrorists? In the Jewish and Christian traditions, we build churches and memorials at places where martyrs died, like St. Peter’s in Rome, or where great numbers of people sacrificed their lives for others, like Normandy or Gettysburg. 

In the Islamic tradition they build monuments to commemorate their great victories. When Muslims swept through the Middle East and Europe they spared towns where people gave over their churches and temples to be converted into mosques. For them a mosque acknowledges the site of a great victory in the name of Allah.

So while some see a mosque near Ground Zero as a commemoration for innocents who died; others could claim it as the place where Islamic terrorists triumphed. The Ground Zero mosque will have an athletic facilities and youth outreach programs, What guarantees do we have that it will never be used, officially or secretly, as a recruitment station for terrorists; that jihadists won’t lurk in the background of its athletic facilities and youth center recruiting potential suicide bombers? 

We know in Great Britain and Germany some mosques are used to recruit suicide bombers. How much more potent would a mosque near Ground Zero be for those bent on jihad against America? Even the head of the terrorist Palestinian group Hamas has come out publicly in favor of the mosque.

Second, where is the money coming from? I’ve known Imam Feisal for years and his rather small mosque in Tribeca shows no evidence of having access to the $100 million dollars needed to build the mosque. 

Where the money comes from is important because with it comes a say on what goes on there. If the donors are rich Kuwaitis grateful that America saved their country in the 1990s, that’s one thing. If it comes from the same people who support Al Qaeda or Gaza-bound flotillas, that’s quite another.

Finally, Imam Feisal Abdul Rauf’s goal is an Islamic Center to promote religious harmony among Christians, Muslims and Jews. It’s been a consistent theme of his since I met him shortly after September 11, at a course he taught at my church in Manhattan. 

His Cordoba Initiative is named after a Spanish city, which in the 8th century was controlled by Muslims and in which the three religions flourished. If Imam Feisal really wants to promote harmony among religions, why not make it an interfaith center – where Christians and Jews as well as Muslims hold religious services? This would guarantee that the peaceful goals of the Cordoba Initiative prevail long after the current controversy subsides.

Imam Feisal needs to address these concerns. But President Obama should stop painting this as a choice between freedom of religion and close-minded bigotry.

Kathleen Troia "K.T." McFarland is a Fox News National Security Analyst, and host of FoxNews.com’s "DEFCON3." She attended a two semester course in Islam taught by Imam Feisal Abdul Rauf at the Center for Religious Inquiry at St Bartholomew’s Church in Manhattan.

Fox Forum is on Twitter. Follow us @fxnopinion.