Fury resurrected him utilizing a program SHIELD had put into place initially in case any of the Avengers managed to get themselves killed in battle. After a sufficient 'recovery time', that is to say, SHIELD doctors making sure that he was well convinced that he hadn't actually died but rather had been sent on a long, restful vacation, he was assigned a squad of agents to work with covertly on Reconnaissance, Recovery, and Infiltration.
Him being alive was strictly on a need to know basis, mostly agents level 7 or above save those with specialized clearance. A few exceptions were made on rankings with Barton and Romanoff, presumably because them knowing would have upset the Avengers dynamic. I can't claim to understand Fury's reasoning, but that makes the most sense.