Freeney hasn't been "figured out," he's just not playing on a unit that can maximize his strengths.
A Tampa-2 front four needs to be able to get pressure on the QB without the blitz or the threat thereof, and usually without a lot of stunting. What you need is a speed demon edge-rusher like Freeney or Simeon Rice and a 3-technique defensive tackle who can get penetration or collapse the pocket on the QB, preventing him from stepping up. Warren Sapp was this guy for Dungy in Tampa, and to a lesser degree, Corey Simon contributed some of this for the Colts last season.
This year, they're without Simon, they let Larry Triplette go, they moved a DE (Raheem Brock) to DT, and they picked up Booger McFarland, who was washing out as a Sapp-stand-in in Tampa Bay. They get no pressure from the inside. Offensive lines know they can easily handle the interior rush, so the tackles can just let Freeney + Mathis rush themselves into the backfield, knowing their QB will be able to step up in the pocket.
If the Colts keep playing the way they've been in the playoffs, this should be even easier next Sunday. To make up for their inability to stop the interior run, the Colts have been pinching their DEs on early downs, sending them into the line of scrimmage, as opposed to their usual playing the run on the way to the pass.
If the Pats offense can have success throwing on early downs, when Brady should have plenty of time, the Colts will have to adjust, and that will open up the run.