Miami Dolphins wide receiver Kenny Stills (10) and Miami Dolphins wide receiver Albert Wilson (15) kneel during the national anthem before an NFL football game against the Tennessee Titans, Sunday, Sept. 9, 2018, in Miami Gardens, Fla.
Trump also tweeted about the protest Sunday, blaming the demonstrations for the league's declining TV audience.
Kaepernick sparked controversy when he sat, then knelt, during the National Anthem before several 2016 NFL preseason and regular-season games.
The NFL passed a new anthem policy in May, but those rules were put on hold to allow the league and union to further discuss the issue.
There did not appear to be any other player protests during the playing of the national anthem before other games Sunday.
Most of the protests came from players who have previously participated, but several prominent activists opted not to join in for opening day.
"Wow, NFL first game ratings are way down over an already really bad previous year comparison", the president tweeted Sunday. "Otherwise worse!" the President wrote. The US President has been highly critical of the players involved in the anthem protests.
NFL Commissioner Roger Goodell announced a revision of its Game Operations Manual on May 23 to include fines for teams whose "personnel are on the field and do not stand and show respect for the flag and the anthem".
"People say your dreams are insane, if they laugh at what you think you can do, good", Kaepernick says in the Nike ad. "The country hasn't moved on from it, so I'm not going to move on from it either". I think we've made progress but obviously we have a ways to go'. "Were trying to move past the rhetoric of whats right or whats wrong in terms of the anthem, and really focus on the systematic issues that are plaguing our communities".