I agree that from a program's point of view within the storyline, the users are godlike. However the concept of an attack on the identity is more something for the viewer of the film to ponder, somewhat outside of the plotline of the film. It's interesting to note that Flynn, a user, never utilizes his identity disk as a weapon. There's no question in his mind who he is, and his identity (in the form of his identity disk) is never challenged. This is just one other thing that sets his character apart as a user.
As a Christian, I find this kind of deconstruction interesting