The flag was identified on social media as the banner of the Islamic State (IS). The black flag has the message "There is no god but God, and Mohammed is the messenger of God" written in Arabic.
Mark Dunaway of Garwood, a suburban town in North Jersey, said he has placed the flag outside his home on Fridays and during Ramadan, the Muslim month of fasting.
"I understand now that people turn on CNN and see the flag associated with jihad, but that's not the intention of that flag at all," Dunaway told NJ.com. "It says 'There is only one god, Allah, and the prophet Muhammad is his messenger.' It's not meant to be a symbol of hate. Islam is all about unity and peace. I am not a part of any group like that, and I'm not anti-American. I love my country, but I am a Muslim."
But Dunaway took the flag down this week after Garwood police officers said they were concerned about his safety. He now has a San Diego Chargers flag in its place.
Marc Leibowitz, who set off the flap this week with a photograph of the flag on Twitter, said he called Dunaway late Wednesday and apologized.
"Our chat was really lovely," Leibowitz said. "I said I'm so sorry and I feel responsible for what had to have been a rough day for him. Seeing all the hateful comments people were directing at him made me worried about what someone might do because of this."