After that summer of mistrust and raw feeling, he's looking on the bright side.
Rauf says he hopes to use the platform he gained through the angry debate to turn his small nonprofit group into a global movement celebrating pluralism.
In an interview Tuesday with The Associated Press, Rauf said he hopes to see interfaith centers like the one he plans to include inside the downtown Manhattan Islamic center built all over the world. Each would be dedicated to fighting extremism and promoting better relations between people of different faiths and cultures.
Already, he said, he is exploring opening facilities in other American cities, as well as in Indonesia and Kosovo.
"We went to the brink, in a certain way," he said of last summer's tumult. But he added, "This crisis showed us what was possible. ... It showed us that there is actually hope. Hope for a better relationship between America and the Muslim world, both domestically and internationally."
Whether there is hope for the proposed center two blocks from the site of the World Trade Center attacks is unclear.
The superheated rhetoric of August and early September has died down, aside from the occasional downtown demonstration, and there appear to be no major governmental obstacles, but the $150 million project still remains on a slow track to construction.
The developer of the site has said groundbreaking is probably three years away. The nonprofit group that would run the center is still being established. A fundraising campaign has yet to begin. Developer Sharif El-Gamal has said he plans to borrow most of the money needed to build by selling a type of bond common in Islamic banking.
The timetable will give Rauf and his wife, the activist Daisy Khan, more time to make their case that a Muslim institution belongs at ground zero. They envision a 13- to 15-story facility with space for a health club, a day care center and playground, an auditorium for cultural events, art studios and galleries, a 9/11 memorial and a two-level prayer room with seating for a congregation of 2,000.
"We were part of the narrative of 9/11," Rauf said, noting that members of his own congregation, based about 10 blocks from the Trade Center, had been victims of the attacks.
"We have an obligation. We have a responsibility" to participate in the rebuilding of the neighborhood, he said. "This center is an anti-9/11 statement."
Convincing the country, though, hasn't been easy.
As city officials declined to block the center, critics, including many prominent Republicans, decried it as a slap in the face to the families of Sept. 11 victims. Newt Gingrich compared the center to Nazis putting a sign next to the Holocaust Museum.
Mayor Michael Bloomberg and religious leaders of many faiths have been among the center's most ardent supporters. Relatives of 9/11 victims have come out on both sides.
The debate took a bizarre turn when the leader of a small Christian congregation in Florida said he would call off his plans to burn the Quran on the Sept. 11 anniversary if the Islamic center were moved farther from ground zero. Rauf agreed to nothing - not even to meet with Pastor Terry Jones - but Jones still ended up changing his mind about burning Islam's holy book.
Rauf and Khan said they have begun talking in recent weeks with more relatives of 9/11 victims in an attempt to build support for the center.
Khan said she hoped some would agree to be "part of the healing process" and help design the center's 9/11 memorial.
The couple are also trying to find a role for themselves in repairing what they see as a rift between U.S. Muslims and the nation's Christian majority.
Mere acceptance of Muslims in the U.S. is not Rauf's goal.
"It is not enough for me that you tolerate me," he explained to an audience in Jakarta last month. "I want you to love me."
The Cordoba Initiative is a pro-Western organization that sent election monitors last spring to Sudan, and Rauf has spent much of his life preaching religious tolerance and the need for people of different faiths to work together.
Rauf and Khan have kept their offices for years in the Interchurch Center, a Manhattan office tower packed with Christian religious agencies that was conceived as a space where different denominations could mingle and collaborate.
His social friends are as likely to be Jewish or Christian as they are Muslim. The Very Rev. James Morton, retired dean of the Cathedral of St. John the Divine, recalled how his family, Rauf, Khan and a rabbi once spent 10 days together on a Mediterranean cruise.
"We went from Spain to North Africa," the Episcopal priest said - a crossing of a historic border and crossroads between the Islamic and Christian worlds. "It was a wonderful trip."
Rauf and Khan said they would prefer to spend their time talking about issues like gender equity and women's rights within Islam. Khan leads, among other things, an empowerment group that favors a more visible role for women in Muslim cultural, religious and judicial institutions.
The couple say they were shocked by the emotional nature of the opposition to the Islamic center project, and regret they did not anticipate the situation ahead of time. Yet they are also insistent that moving the facility to another location would be a mistake.
The couple's courtship of 9/11 families appears to be aimed at potentially influential fence-sitters in the debate over the center, rather than ardent critics, although Khan also recently participated in a public panel discussion with Jim Riches, a former New York City deputy fire chief whose son, Jimmy, was killed at the trade center.
"It was a true dialogue," Khan said of her appearance with Riches. "When he was speaking about his pain, I had tears in my eyes."
She said the main point she wanted to get across during their talk was that the 9/11 attacks were an epic tragedy for Muslims, too - compounded by fears of a backlash and a sense that they had been irreparably alienated from their countrymen.
"The fact that we were not allowed to participate in this tragedy, that we were shut out ... that was very traumatic for the community," she said.
Establishing a presence so close to ground zero, she said, would send a powerful message: "We stand for peace, and peace where it matters the most."
And if the structure never gets built, due to financial problems or political difficulties?
"It certainly matters, but it will not be an impediment," Rauf said. His work will continue, although, as Khan added, "It is a lot easier to bring people together in bricks and mortar."