As Michael told Tom just before he left Tahoe following the shooting: "Right now, you're the only one I can completely trust...[Neri and Rocco] are businessmen; their loyalty is based on that." In other words, even though Michael was nearly certain at that point that Roth was behind the shooting, he couldn't be completely certain that Neri wasn't involved in the shooting somehow.
Michael, subtle fellow, might have been playing his uncertainty about Neri to good advantage with Roth. By using Buscetta as his bodyguard, and leaving Neri out, Michael might have been signaling Roth that he was still in the dark about who was behind the shooting--in other words, not merely that he didn't completely trust Neri,but that he might actually suspect Neri (and not Roth).