Trump called for the NFL to "fire or suspend" those who kneel during "The Star-Spangled Banner."
"If NFL fans refuse to go to games until players stop disrespecting our Flag & Country, you will see change take place fast. Fire or suspend!" Trump tweeted on Sunday, which followed similar comments he made Friday at a rally in Huntsville, Alabama.
Brady, who has said that he's friends with Trump, spoke out Monday, saying, "I certainly disagree with what he said. I thought it was just divisive."
After Trump's comments, players on various teams took a knee together on Sunday or stayed in the locker room during the national anthem.
Brady, 40, was interviewed on WEEI's "Kirk and Callahan" show Monday morning, one day after he linked arms with his fellow Patriots to show unity.
"Like I said, I just want to support my teammates," he said of his actions. "I am never one to say, 'Oh, that is wrong. That is right.' I do believe in what I believe in. I believe in bringing people together and respect and love and trust ... I have been blessed to be in locker rooms with guys all over the United States over the course of my career ... The one thing about football is it brings so many guys together — guys you would never have the opportunity to be around."
Brady said what makes a football team so special is that "we're all different."
"I think everyone has the right to do whatever they want to do. If you don’t agree, that is fine. You can voice your disagreement, I think that is great. It’s part of our democracy. As long as it is done in a peaceful, respectful way, that is what our country has been all about," he continued.
Brady followed in the footsteps of another Trump friend, Patriots Chairman and CEO Robert Kraft, who released a statement Sunday saying how "deeply disappointed" he was "by the tone of the comments made by the president."
"I am proud to be associated with so many players who make such tremendous contributions in positively impacting our communities. Their efforts, both on and off the field, help bring people together and make our community stronger. There is no greater unifier in this country than sports, and unfortunately, nothing more divisive than politics," Kraft said.
The taking of a knee by NFL players began last year when now former San Francisco 49ers quarterback Colin Kaepernick declined to stand during the national anthem before a preseason game against San Diego.
He later explained to reporters that he was doing so to peacefully protest until there is "significant change" on racial oppression in this country.