Because SHIELD turned out to be a militarized police force which neo-nazi Hydra corrupted(Captain America: The Winter Soldier) from the inside,
which neo-nazi Hydra corrupted from the inside (Captain America: The Winter Soldier),
using SHIELD to create weapons of mass destruction (The Avengers/Avengers Assemble: Steve Rogers finds weapons based on Tesseract) and planned on killing people for potentially being dangerous to the new world order(Captain America: The Winter Soldier).
killing people for potentially being dangerous to the new world order (Captain America: The Winter Soldier).
At the end of Avengers: Age of Ultron, Fury's SHIELD acted as peace keepers and rescuerescuers, saving people, not policing them.