Alex Smith is absolutely right about one thing. He has been through a lot worse than the 49ers' flirtation with Peyton Manning and his own on-again, off-again, on-again courtship with his franchise.

Name a body part. They've all been bruised or broken. Shoulder. Knee. Ankle. Heart. Guts.

Smith's toughness has been publicly questioned by former coaches. His leadership skills have been minimized by offensive coordinators and a few teammates. He has been benched, he has been booed, he has been dismissed on too many occasions to count.

Then, when he finally wins, he learns about his club's backdoor play for Manning.

"Not offended at all," the veteran quarterback insisted on a conference call Wednesday after securing a three-year, $33 million contract. "Obviously, it was a little unexpected, but that's part of the deal. I relished the opportunity to compete for the starting job with Peyton Manning."

You buying this? Save your coin. There isn't an athlete in pro sports who wouldn't be seething, wounded and increasingly distrustful of his bosses. Those chummy Smith-49ers family ties have been severely strained.

Smith, 27, wanted to share reps with Manning about as much as John McCain wants to share meals with Sarah Palin.

After leading the 49ers into the NFC Championship Game during coach Jim Harbaugh's rookie season, Smith assumed the team's goal of acquiring game-changers coincided with his own thoughts – obtaining players (Randy Moss, Mario Manningham) who run the right routes and catch the deep passes. He expected to finalize a new agreement with the 49ers in a relatively short period.

"The contract was out there the whole time," Smith said. "I feel like I've earned it."

Yet if Manning had chosen the 49ers over the Denver Broncos, Smith would have been the odd man out, not wanting to be here, and not wanted by the organization, either. The 49ers would have yanked that three-year contract faster than you can type Colin Kaepernick. The lanky, flame-throwing backup would have been groomed by the future Hall of Famer, though the timeline was contingent on Manning's surgically repaired neck. One year? Two years? Three years?

That was the most curious element about this supposedly private wooing of Manning. Put five orthopedists in a room and you'll get five different diagnoses and prognoses. We're talking about four neck surgeries, one aging body, and a price tag closing in on $100 million.

Granted, any team that signed Manning would have protected themselves legally and financially. And maybe his acquisition would have been fine with either Broncos or Titans fans, neither of whom expected to contend for a Super Bowl with their current talent.

But the 49ers came within minutes of the Super Bowl. Why enter into the danger zone? Why jeopardize what works? The superb defense returns largely intact, wideouts Moss and Manningham upgrade the weakest position, and Harbaugh – a deserving Coach of the Year as a rookie – figures to be even better in his encore.

Now, though, Harbaugh has some rehabbing to do. He has a quarterback to heal, bruised feelings to soothe. His human touch has descended like a jackhammer. He devoted months to nurturing Smith, earning the quarterback's trust and transforming him into a confident, effective leader who guided the team to a 13-3 regular-season record.

Smith will never be Aaron Rodgers or Tom Brady or Manning. But he doesn't make those spectacular throws against the New Orleans Saints and New York Giants if Harbaugh hadn't convinced him that he could be special, that he could win, that he was the 49ers' guy.

"I never really felt like a free agent, to tell you the truth," Smith said. "This was the plan, to come back here. It was a matter of getting it right and getting it done."

Still, Smith has to be wondering whether his coach envisions him as a caddie, whether their pairing at Pebble Beach was a play for the cameras, whether all that chest-bumping and high-fiving and talk of family ties was all a bunch of hooey.

Smith is smart and resilient, and he undoubtedly will recover. But in sports, as in life, this is known as a setback.

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