The one big reason the 49ers aren’t going to play Colin Kaepernick

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The chants rang out from the sparse and quickly thinning crowd at Levi’s Stadium as clear as the Thursday night sky:

“We want Kap!”

Who could blame the fans for chanting? The 49ers looked terrible in a nationally televised 33-21 loss to the Drew Stanton-led Arizona Cardinals.

Starting quarterback Blaine Gabbert wasn’t the sole reason the 49ers lost Thursday’s game, but he wasn’t doing much to help the cause either. And anyone who has watched the 49ers this season can see that Gabbert isn’t capable of running the read-option looks first-year head coach Chip Kelly wants to run.

Frankly, it looks like the 49ers, who are now 1-4 on the season, are running an offense built for Colin Kaepernick with Gabbert.

So why aren’t the 49ers playing Kaepernick?

Well, the Niners have more than 14 million reasons to keep No. 7 on the bench.

If you want to believe that Kaepernick isn’t playing as a retribution for his national anthem protests, you have to do so with the understanding that such a belief is not rooted in fact or logic. The 49ers have been supportive of Kaepernick’s cause — Kelly has defended him vehemently when prodded in press conferences and team CEO Jed York has donated $1 million to a charity he believes fits Kaepernick’s mission. Also, by all accounts in the Bay Area, there’s no division in the 49ers locker room over the anthem protests.

With all that being the case, the 49ers would then turn around and punish Kaepernick by not playing him? If that’s the case, that’s some black-belt-level passive aggressiveness.

If the 49ers didn’t want to play Kaepernick because of his stance, they would have cut him in the preseason. They didn’t do that because, frankly, they couldn’t — the quarterback roster was too thin.

Oh, and they basically already had paid him his full salary for the year.

Kaepernick is going to get the same check for 2016 whether he’s on the roster or not, and while there was some thought as to whether it’d be more prudent for the 49ers to use his 53-man roster spot on another player, the team decided it might as well keep the guy it already paid around — he has experience and as far as emergency backup quarterbacks go, he’s not a bad option.

But that’s all Kaepernick is to the 49ers — the emergency backup. The only way he’s going to see the field is if Gabbert is injured.

At this point, though, with whatever ridiculous postseason hopes the 49ers might have held extinguished and third-string quarterback Christian Ponder better versed in the playbook, the 49ers could cut Kaepernick.

They won’t do that because of the political backlash that would follow. It’s not worth it to sign some scrub off the street. They’ll wait until the offseason, when you can cut the guy who didn’t take a snap the entire season with some level of impunity.

So why don’t the 49ers use him now? They paid him and they can’t cut him — they might as well use him, right?

Wrong.

Kaepernick burned the 49ers last season after he injured his shoulder in the early part of the year and played through the injury until he was benched forpoor play.

Kaepernick didn’t exactly engage in a rehabilitation plan that would get him back on the field immediately and he waited to have surgery on his shoulder, knowing that if he made it to April 1 and he wasn’t fully healthy, the 49ers would have to pick up the full $11.9 million he was owed in 2016. Kaepernick had the NFLPA ready to pounce if push came to shove.

It was a shrewd and a bit nefarious move by Kaepernick and it worked.

Kaepernick missed the first two games of the preseason recovering from that surgery, too, and by the time he played (poorly), the anthem controversy was full bore and the 49ers didn’t have much of a choice but to keep him — unless they wanted Jeff Driskel to be their backup quarterback.

But if the 49ers put Kaepernick on the field for any reason this season, they risk him getting injured and remaining that way until April 1, when he’d be guaranteed $14.5 million for 2017.

Perhaps that we-have-no-choice scenario comes to pass, but in the meantime, the Niners are going to bide their time until they can cut Kaepernick.

So unless Gabbert’s arm is dangling in its socket and Ponder is locked in the bathroom, Kaepernick is going to remain on the bench this season.

It’s not politics — it’s business.

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