SAN FRANCISCO — They already knew how far they had come, and they surely knew and appreciated how far he had come.

On Sunday the 49ers received an unsparing assessment of how far they still have to go — and, moreover, how far they could reasonably expect quarterback Shaun Hill to take them.
Hill is smart, resourceful, meticulous and usually accurate, unlikely to lose games or stink it up enough to make 49ers fans try to bury him under an avalanche of boos.
He is not, however, a genuine franchise quarterback, capable of overcoming an offensive line equally defective at blocking for the pass or the run.
Insofar as the 49ers were victims of a 45-10 drubbing by Atlanta, Hill certainly couldn’t do anything about the six touchdowns and 477 yards the Falcons accumulated.
But one of the many things the 49ers and 69,732 at Candlestick Park learned is how to recognize a franchise quarterback. He has an unmistakable sense of composure and command. He can recognize and exploit defenses. His arm is strong and accurate, able to hit targets all over the field.
In short, he looks a lot like Matt Ryan, Atlanta’s second-year quarterback whose first half — 15-of-21 passing for 258 yards and two touchdowns — put away the 49ers. His rating in the first half (144.5) was considerably more than consequential than his rating (110.0) once his garbage-time stats were added.
Hill, by contrast, had one of his worst games ever — and took his first home loss in eight starts.
“When we see the film I’m sure we’ll find out more, but I know I left a few plays out there,” Hill said. “When you lose a game like this, you’ve got to look at the quarterback first.”
To look at Hill on this day was to see a quarterback who all too often looked confused, like the backup he was for the first four years of his NFL career, in Minnesota.
Coach Mike Singletary came to his defense, saying Hill was “running for his life.”
Though this is mostly true, Hill also threw an assortment of passes that should never come off the hand of an NFL starter. He was not as absurdly bad as Raiders quarterback JaMarcus Russell has been, nor was he much better.
Hill was bad enough to be critically aware of shortcomings, so much so that he occasionally lost his usually firm grip on his composure.
“I was not agitated with my teammates or players or anything like that,” Hill said. “I was agitated with myself at times, agitated with the way things were going, perhaps. Most of that frustration was toward myself.”
In the first half, when the numbers could have mattered, Hill completed 6 of 17 with one interception (on a tipped pass). In the second half, when not much mattered, he completed 9 of 21, with no picks.
He threw behind tight end Vernon Davis, wide to tight end Delanie Walker, short to wideout Isaac Bruce and well over the head of wideout Josh Morgan.
Hill played as if in a fog, as if daydreaming about the day when rookie wideout Michael Crabtree — on the sideline wearing black sweats and red shoes — actually suits up and becomes a playmaker.
Now it would unfair to drop this entire mess in Hill’s lap. San Francisco’s limitations were laid bare, from its ineffective offensive line to its general lack of speed on offense, from its vulnerable secondary to the possibility that this bunch was a bit too impressed with its new and improved self.
Yet Hill has been the most stable thing about the offense and the team. His story, rising from unheralded backup to solid starter, has inspired. He has been unflappable, worth his weight in intangibles, even if he is wrapped in plain brown paper.
Maybe this was a one-game glitch, Hill on edge and off rhythm after being hit so often. Or maybe this is what happens against a Falcons staff and team with two weeks to study strengths and weaknesses and tendencies.
More likely, this is a sign that disrespect of San Francisco’s run offense leaves it up to Hill to win games with his arm. Quite an imposing challenge for a passer easily defended and without fabulous receivers.
If the 49ers didn’t already know their limitations at quarterback and, by extension, on offense, they do now. Until they find a running game, perhaps upon the return of Frank Gore, those limitations aren’t going anywhere.