Eric Branch of the San Francisco Chronicle reported Lynch said he regretted saying "divisive" and that "he not only respects players' right to protest, but understands the motivation" during an appearance on KNBR Radio's morning show Friday.
Lynch's comments come two days after he had this response to reporters when asked about his stance on protests from players during the national anthem, via ESPN's Nick Wagoner:
"And I think this game brings people together. So I think personally when I see that, I think that's divisive. And I understand guys see things and they're not happy. They have that right. And I think we'll always respect people's rights. That doesn't mean I believe that. I believe this game should be celebrated for what it is. I think [it's] a tremendous unifier for our country and for the way things should be."
The 49ers were at the center of the national anthem protests last season when quarterback Colin Kaepernick took a knee before games to show his objection to racial inequality in America.
Kaepernick's movement led to players throughout the NFL using their platform to start their own protests, whether it was by taking a knee, locking arms as a team or raising their fists in the air.
Philadelphia Eagles defensive end Chris Long showed support for teammate Malcolm Jenkins, who raised his fist prior to Thursday's game against the Buffalo Bills, by putting his arm on Jenkins' shoulder.