The court shown in the original commercial is hearing arguments in the city of Detroit's bankruptcy case.
The city, owing billions of dollars to creditors and faced with a slumping tax base and steady population losses, filed the nation's largest municipal bankruptcy case in July 2013.
City employees and retirees face the prospect of wage, benefit and pension cuts as part of any bankruptcy settlement.
The Detroit News published a story on Friday about the commercial and the negative response it was receiving in Detroit. Just hours later, Honda officials told the newspaper that they would be removing the images of protestors.
"The slight change we made to the commercial simply reflects our desire to remove anything that would get in the way of our uplifting message," Honda spokesman Steve Kinkade told Automotive News on Saturday. "The original commercial obviously was not intended to represent Detroit or the challenges experienced by the city, its people or our industry."
The Rev. Charles Williams II, president of the National Action Network's Michigan chapter, told the News that the original ad was a slap in Detroit's face.
"They're using our pain for their pleasure to promote Japanese automobiles while we are suffering in part because of the decline of American automobiles from foreign automakers," Williams told the paper.
Kinkade said the spirit of the commercial was intended to serve as a positive expression for everyone and the "incredibly positive response" it has generated reflects these intentions.
"Honda has operations and personnel in the city of Detroit and elsewhere in the metro Detroit area and we continue to be actively engaged in a variety of community outreach activities in the city," Kinkade said. "We're pleased Honda is playing a role in the continued comeback of the city."