The San Francisco 49ers have decided not to let a small controversy affect Colin Kaepernick's roster spot with the team.

The quarterback made the 49ers final roster that was announced on Saturday. The team cut a total of 20 players so that they could get down to the NFL mandated 53-man limit by 4 p.m. ET.

The 49ers had four quarterbacks on their roster going into Saturday, and it was pretty clear that at least one of them was going to cut. In the end, coach Chip Kelly decided to dump rookie Jeff Driskel and keep Kaepernick.

The move by Kelly wasn't a complete surprise. The 49ers coach has said all along that if he kept Kaepernick, it would be a football decision that would be unrelated to his protest of the national anthem. In the week leading up to cut day, Kelly made it clear that he thought Kaepernick was one of the two best quarterbacks on his roster.

The decision to keep Kaepernick raises some interesting questions going forward.

For one, Kaepernick's contract now becomes an issue. If the quarterback plays at all in 2016 and gets injured, then his 2017 base salary of $14.5 million would automatically become guaranteed.

Kaepernick also receives a $125,000 bonus for every game that he's on the team's active roster, so if the 49ers decide to deactivate him on game day -- and go with Christian Ponder as their No. 2 QB -- then the team could save $2 million in bonus money ($125,000 x 16 games).

Of course, Kelly doesn't think like a front office guy when it comes to contracts, so don't expect him to deactivate Kaepernick just to keep him from earning a game day bonus.

#49ers Chip Kelly: Right now Blaine is No. 1 and will start vs. the Rams. Kap is No. 2. Only ones to be active on game day. — Cam Inman (@CamInman) September 3, 2016

As Kelly said on Saturday, Kaepernick will be the team's No. 2 quarterback behind Blaine Gabbert for the team's season opener on Sept. 12 against the Rams.

Anyway, besides the contract, keeping Kaepernick also means that the 49ers are also going to have deal with the controversy that comes with him.

Kaepernick's decision to protest the national anthem has become a scorching hot topic in America.

"There's a lot of things that need to change," Kaepernick said on Aug. 28. "One specifically? Police brutality. There's people being murdered unjustly and not being held accountable. People are being given paid leave for killing people. That's not right. That's not right by anyone's standards."

The 49ers quarterback has said that one of the big reasons he's protesting the national anthem is because he has an issue with the police brutality that's going on unchecked in this country.

That statement didn't sit well with the Santa Clara Police Officer's Association, and that group has now threatened to pull officers from working 49ers games at Levi's Stadium.

Of course, even though Kaepernick's on the team now, the 49ers could change their mind at any point and cut him sometime down the road.