Yes, Tommy Elliot is posing as Bruce Wayne after the events of Heart of Hush. Alfred, Dick, Damian and all the Batman-related heroes are not really "cooperating" with him. Rather, it's a relation of mutual benefit, a quid pro quo: Hush is allowed to be publicly seen as Bruce Wayne and (limitedly) benefit from the Wayne fortune, and the Bat-family is able to directly monitor Hush's movements and scheming. Besides, with the real Bruce temporarily gone, having Hush "play" him before the cameras eases any possible suspicion anyone may have. 
 
My two cents? In the end of House of Hush, Tommy Elliot is involved in an accident that scars his face enough to avoid any confusion with Bruce Wayne, but making him use his Hush bandages again. Full circle.

Short version is that they tried to lock him up but he got out so now they have an uneasy truce where he keeps "Bruce" alive to the world and the Bat Family babysits him to prevent him from doing anything nefarious... which we know he's managing to do anyways.