An analysis of the challenge call is up at http://www.grantland.com/story/_/id/7232735/this-game-inches
Bill Barnwell: basically, it's a brilliant call.
1. Because it gives our defense a breather
2. There's a small chance that either Manningham did bobble it or that the refs blow the call.
3. (Here's the true genius of it) You can't take challenges with you. Our timeouts were not going to be a factor, and all challenges 2 min and in, or in OT, are automatic. So it makes total sense to burn a challenge on any late game critical play. There's literally no downside to it, and yet coaches decline to do it all the time. And then they finish the game with two meaningless challenges in their pocket.
I honestly feel that (some) coaches don't follow this challenge strategy because they're afraid of being embarrassed. And that's a form of egotism too - putting your own reputation before the team's chances of winning. People who call Harbaugh an egotistical guy should ponder that.