Now, Kaepernick is back in the pages of the magazine, this time as one of its 100 most influential people of 2017. In an interesting twist, Jim Harbaugh, Kaepernick's former coach with the 49ers and head coach at Michigan, wrote the essay explaining why Kaepernick landed on the list and praising his efforts.
"I thank Colin for all he has contributed to the game of football as an outstanding player and trusted teammate," Harbaugh writes. "I also applaud Colin for the courage he has demonstrated in exercising his guaranteed right of free speech. His willingness to take a position at personal cost is now part of our American story.
"How lucky for us all and for our country to have among our citizens someone as remarkable as Colin Kaepernick."
Harbaugh's essay represents a change in tone from his initial reaction to Kaepernick's protest. Soon after Kaepernick's protest became public knowledge, Harbaugh said "I acknowledge his right to do that, I don't respect the motivation or the action."
Harbaugh later clarified those comments in a tweet, apologizing for misspeaking and saying that he supported Kaepernick's motivation but it was the method of action that he took exception to.
In a February podcast interview with the San Jose Mercury News, Harbaugh told columnist Tim Kawakami that he had taken more time to reflect on Kaepernick's protest and had better understanding of why Kaepernick did what he did.
Kaepernick played for Harbaugh from 2011 to 2014 before the Niners parted ways with Harbaugh. Kaepernick is currently a free agent after electing to opt out of the final year of his contract in San Francisco. He will not return to the 49ers after they signed veteran free agents Brian Hoyer and Matt Barkley. Barkley has already been issued Kaepernick's No. 7.
Meanwhile, Kaepernick reportedly plans to stand for the national anthem in 2017 and continues to donate money through his foundation to various causes that support his mission to fight social injustice. He has four months remaining in his donation schedule, with donations currently at $600,000 out of the $1 million he has pledged.
Kaepernick's lack of a job in the NFL has been the subject of much debate this offseason with some arguing that he's being blackballed for his political stances and others arguing he's still available solely for football reasons.
Harbaugh has also taken the opportunity to argue that Kaepernick is still capable of playing winning football in the league.
"I think he's an outstanding player," Harbaugh told NBC Sports radio. "I think he's a great competitor who's proven it in games and has the ability to be not only an NFL starter but a great NFL player.
"... Colin will be just fine. He'll just keep plugging away, and I think you'll see he'll have a great career and be a great quarterback. Win championships."