Why? He's still got age on his side...really started to come into his own the last season and 1/2...could really benefit from a fresh start with a new team.
Tom Brady, Peyton Manning, Andrew Luck, et al are rare finds...odds are we will never get one. We can win a championship with a good, solid quarterback who doesn't turn the ball over, can complete more than 50% of his passes, and who is motivated to show the league that San Fran made a mistake in how the used them, and in letting them go.
I'll take him as a longer term option over an unproven entity (be it a Flynn, or a draft pick) any day. I'm sick of crossing my fingers and hoping someone is going to develop into something halfway decent.