The president vowed to give communities greater say in refugee policy and discussed reducing the refugee resettlement program. Minnesota, which is home to a large Somali immigrant population, also has the largest number of refugees per capita nationwide, with 13 percent of the country's refugees, according to U.S. Census data.
Frey took to Twitter to hit back, writing that immigrants and refugees are welcome in his city.
Before the rally, Frey had issued a proclamation declaring Thursday "Love Trumps Hate" day in the city.
Appearing on "Fox & Friends" with hosts Steve Doocy, Ainsley Earhardt, and Brian Kilmeade, Homan agreed with the president's message.
He told the "Friends" hosts that Frey is "not a dictator."
"He works for the taxpayers of that city, and the taxpayers have the right to decide," he said. "They pay school taxes. They pay property taxes. They should have a say in how that city runs."
"So, shame on him," said Homan. "I'll tell him the same thing I told Representative [Pramila] Jayapal. They work for us, but they forget that."
The Trump campaign blasted Frey earlier in the week after city officials proposed a fee of more than $500,000 for security at the Target Center for the rally.