Superheroes who signed the Registration Act had the option of choosing to work for S.H.I.E.L.D., and the organisation under acting director Maria Hill was largely responsible for enforcing the Act. When the war is over, Tony Stark is appointed the new director of S.H.I.E.L.D., with Hill demoted to being the deputy. Thanks to the rather fantastic story tie-in between Captain America: Civil War and Agents of S.H.I.E.L.D., this is no longer really a possibility. The infiltration of the agency by Hydra was revealed, and for all official intents and purposes, S.H.I.E.L.D. as an organisation doesn't really exist. Of course they're still out there working in the shadows, led by Phil Coulson, but they're not in a position right now to be trusted again by the government or US citizens. While it's expected that the series will tie-in with Civi War in some way or another, it would take a lot of work in the episodes between now and then to restore S.H.I.E.L.D. back to its former position whereby it could be heavily involved in the official side of things, and where Tony Stark would be appointed its director.