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Are you just trying to compile robot_pose_ekf? If so, try installing ros-indigo-bfl (sudo apt-get install ros-indigo-bfl) as you might be simply missing the dependency.

If you're trying to build your own package against BFL, check out the CMake in robot_pose_ekf: https://github.com/ros-planning/navigation/blob/indigo-devel/robot_pose_ekf/CMakeLists.txt as it definitely builds against BFL in indigo, and as far as I know, it is the only released package that depends on BFL.

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