The 49ers’ 2013 season ended in the worst possible way on Sunday. A lot of questions face this team as the players clean out their lockers and the front office prepares for the upcoming draft rather than the Super Bowl. Will they lose Greg Roman, Vic Fangio or Jim Tomsula? Is the Frank Gore era coming to an end? Will Trent Baalke be able to maneuver the handful of costly extensions due for the young core of talent on this team?

It’s hard to see the forest for the trees, and the 49ers crashed into a damn ugly one on Sunday. The sting of this game will linger, and the local media has more than enough salt at the ready.

  • The new kids on the block over at the flagship of the Raiders are brimming with HOT TAKES ON COLIN KAEPERNICK’S WARDROBE.
  • The Cohn Zone pushed all of its chips into the table by boldly proclaiming that its wildest dream had come true, and now the 49ers are in bits and pieces all over the kitchen floor.
  • Scott Ostler asks, “did anyone hear the 49ers’ window of opportunity slamming shut?” Harbaugh answered a question about that yesterday. “I don’t understand windows,” said the 49ers head coach. “It’s confusing in terms of football. So, back today competing.”
  • Ann Killion believes “the seeds are being sown for a potentially disgruntled Harbaugh” and that Colin Kaepernick’s contract negotiations “could rankle him.”

The internet is filled with vitriol over the team everybody suddenly loves to hate, with comparisons to the ’90s Buffalo Bills and enough schadenfreude to crash memegenerator.com

But it’s ironic — just as radio stations and Bay Area sports websites benefited so much from the 49ers recent success, these same outlets are just as Pavlovian over this season’s disaster of an ending. Columnists and talking heads who’ve complained about being slighted by the 49ers for their standoffish media tactics in the past are smelling blood in the water now. They’re trying to tell us that the sky is falling, but don’t waste your time on that bomb shelter.

On a microscopic level, a third-straight trip to the threshold without crossing it makes a fourth seem like mission: impossible. The 49ers have been hot at the craps table for three years now, and every single time they’ve been a roll or two short of cashing out. Except the 49ers aren’t playing the game blind — they’ve got experts, and they’ve got the advantage needed to get back to the table again.

Sustainability in the NFL seems to be predicated on three crucial pieces: a smart general manager, a terrific coach and a franchise quarterback.

Trent Baalke

He has his faults — his A.J. Jenkins gamble failed, along with the rest of his 2012 draft — but for every Jenkins there’s an Aldon Smith, and most draft classes can’t be successfully evaluated for at least three years. We’ll see how Tank Carradine and Marcus Lattimore pay off, but for now this team has his fingerprints all over it. Several of the expiring contracts that could handcuff the 49ers have his draftees names on them. In free agency, he’s made calculated decisions (see: Justin Smith’s contract extension to bridge the gap to Tank Carradine and not competing for Dashon Goldson before a safety-heavy 2013 NFL Draft), he’s continued to stockpile draft picks and he’s maneuvered contract extensions to leave some salary cap breathing room.

Jim Harbaugh 49ers press conference

Jim Harbaugh

He makes $5 million a year, which puts him third in the NFC West behind Pete Carroll and Jeff Fisher (who both make $7 million annually). Without his contributions, none of the sweeping expansions the 49ers are experiencing would have happened. The 2011 resurgence spurred the stadium construction, which in turn spurred several blockbuster partnerships and earned the Yorks a whole lot of money. Harbaugh is 50 years old (Pete Carroll is 62 and Bill Belichick is 61, for comparison), which means he’s got a lot of coaching left in him. Does anyone really believe this organization will let him slip through their fingertips? Please.

Colin Kaepernick

He’s 26 years old and just finishing his first full season as the 49ers’ starting quarterback. In that season, he passed for over 3,000 yards, threw 21 touchdowns to 8 interceptions and finished seventh in average yards per attempt (7.7). His damning final decisions in the Super Bowl and NFC Championship Game showed his youth, yet the 49ers wouldn’t have been in either game without him. Kaepernick is eligible for a contract extension starting this offseason, and when he gets it, it’s going to be substantial. A quarterback getting “rankled” sounds like a lovely narrative, and I’m sure the comments section in Killion’s post is rife, but a narrative is all that is. File that in the same folder as “press conference attire” and ignore it.

What happens with the rest of the team will be spelled out in the coming months:

– Donte Whitner, Anquan Boldin, Anthony Dixon and Tarell Brown are just a few players who could use their performances on the 49ers as a springboard to gigantic contracts with other teams. But the 49ers faced similar personnel problems last offseason — Goldson, Delanie Walker and Isaac Sopoaga all got paid — and this 2013 team is the best we’ve seen in the Harbaugh era.

– Then there’s the NaVorro Bowman injury, and that’s a big one. But reinforcements are coming, and the way the 49ers have recruited backup linebacker talent over the last few years (Larry Grant, Michael Wilhoite, Dan Skuta, Corey Lemonier … ) gives no reason to doubt they can find a suitable stopgap.

Certainly there is work to be done, but this team has steadily improved for three years now. Super Bowl trip or not, Gore wasn’t getting any younger. Super Bowl trip or not, impending free agents were going to test the market. Super Bowl trip or not, Harbaugh and Kaepernick both excelled enough to deserve raises. What happened on Sunday changed nothing about the state of the 49ers going into this offseason, no matter how much disgruntled Bay Area columnists want you to believe it did.