Are 49ers less interested in extending Trent Brown after injury?

I sort of figured that the San Francisco 49ers would, naturally, extend right tackle Trent Brown to a long-term contract just as soon as they could. He’s developed into a great starter, but has missed two the team’s last three games with a shoulder injury and, apparently, not everyone is happy about that.

In one of his Q&A columns, Matt Barrows of the Sacramento Bee was asked if the 49ers were unhappy that Brown didn’t play on Sunday, and if that puts him on “rocky roads” with the team going forward (the user also suggested that Matt Maiocco alluded to this, though I couldn’t find where this took place).

Barrows’s response:

I’d go a step further and say the 49ers were disappointed he didn’t play against the Seahawks, too. … I don’t know how much this affects negotiations. It’s safe to say they are to some degree less gung-ho about inking him to a new deal than they were pre-injury.

Kyle Shanahan did word things in something of an odd way when asked about Brown’s injury, saying that the player hadn’t yet informed the team of his intentions. He talked like he was out of the loop and not in on the decision, which is fairly uncommon from what I can tell.

But it’s what Barrows says that is the driving force behind this, as far as I’m concerned. Shanahan’s choice of words could mean absolutely nothing, but Barrows knows what he’s talking about, so this is definitely a concern. Brown is a great, young player, and it would be a shame if something like this could ruin his potential future with the team.