According to the conversations between the ATC and the chopper, the chopper pilot had the aircraft in sight and asked for visual separation...meaning they would route around it visually.
As the two aircraft get closer to each other, an air traffic controller checks in with the military helicopter, asking the pilot, "PAT25, do you have the CRJ in sight?" The air traffic controller then tells the helicopter pilot to "pass behind" the American Airlines jet.
The helicopter pilot checks in, saying that the plane is in sight and again requests "visual separation," which is granted. But the two aircraft continue on the same path. Seconds later, gasps and shouts can be heard from the air traffic control tower as the helicopter and jet collide.
Obviously, whatever they were looking at, it wasn't the airplane.