First, back in 2013 the guy signed a big-time team friendly deal - 8 year / 110 million. If he wanted to hit the open market he could easily have blown through that, unless you haven't been paying attention to how money is being spent in MLB recently.
Second, this year is maybe slightly above league average offensively but he is still as good defensively as any 2B in the game. There is no one who turns a DP better than Pedroia. Did you see the game last night? Hard hit ball close to Nunez that he doesn't get allowing the bases loaded in the 8th? Pedroia has made that play in his sleep his entire career. If Reed gives up a granny to lose the game last night, all anyone would be talking about is Reed, not Nunez. It's the little things that go unnoticed sometimes, but you would think that an alleged Sox fan would have realized how big Pedroia plays in the field over the years.
Third, its not his fault that Machado decided to slide 2 feet from the bag and go right into his knee. He used to have hand issues but to his credit he has stopped with the dumb slides into 1B.
If he was fully healthy this year he'd still be a top 5 or at worst a top 10 2B in the game. Don't blame him for Machado's dirty crap.