49ers rookie wide receiver Jacob Cowing was at risk of losing his job as the punt returner.

He muffed a punt in the upset loss to the Vikings. The 49ers ended up recovering it, but a mistake like that from a rookie usually is enough for head coach Kyle Shanahan to pull the plug on that player. Shanahan hasn’t been known to be patient with rookies or young players.

However, it seems his patience with these players has increased a bit. On Wednesday, Shanahan clarified that the 49ers won’t relieve Cowing as the punt returner.

“It’s one muffed punt. Just when it comes to catching stuff, he’s been as natural of a catcher as we’ve had in our eight years here just in practice and how he’s been in the games,” Shanahan said. “I know that one got away from him, which we can’t have those, but everyone muffs one here and there. You just hope that was the end of it.”

As soon as Cowing let the ball slip through his hands, I automatically believed he was done. He was never going to be the punt returner again for the 49ers. Again, Shanahan runs a zero-tolerance policy with rookies and young players. It seemed like a guarantee that Cowing was done.

For Shanahan to give Cowing that leeway indicates his growth as a coach. Or perhaps he is a big believer in Cowing to correct it and not let it occur again. Whatever the case, this is a great way to instill confidence into Cowing. He has his head coach’s backing despite the mistake.

You have to wonder if the Vikings recovered the muffed punt Shanahan would have a different tune. Maybe it is also the fact that the 49ers are slim on options behind Cowing for punt returner. So, he’s their best bet to give them production and make correct decisions.

Shanahan giving Cowing that leeway could also be because he will be utilized in the offense in Week 3. With Deebo Samuel out, the 49ers will need another wide receiver to step up. Cowing is the only player they have that can fill in. It doesn’t make sense for Shanahan to remove him as a punt returner, which would hurt his confidence.

He needs Cowing to be headstrong with opportunities looming for him in the offense. Either way, I sincerely doubt that Cowing will be forgiven if he muffs another punt soon, especially if the 49ers don’t recover it.