Ezra Klein has a good rundown on the problem with fact checking organizations in today's political climate and partisan arena. It boils down to the fact that they can't manage to stay out of the he said she said model of reporting that fact checking ostensibly should be immune to.
Take a look at the whole thing, it'll only take you a couple of minutes.And that, ultimately, is the problem with the fact checker model. They have no actual power, so their only influence comes from the public’s sense of their legitimacy. And about half of the public leans towards one party and about half of the public leans toward the other. That means PolitiFact and these other outlets need to find some uneasy balance between the parties, too. But that just means the parties will have plenty of opportunities to decide that these are hackish, partisan operations. Conservatives got there a few weeks ago, and now liberals are following.
And remember everyone is entitled to their own opinions but not their own facts.