"The Matrix" is a brilliant allegory about all things concerning the perception of reality. It's a great tool we can always use to distill and abstract more precisely that specific subject. Other than that, to think we actually live in a simulation shouldn't be a concern in itself, for that simulation has then to be built upon something else. People have the tendency to think that if they only frame the simulation, then that's all existence can be about, and the mental distance they establish from the "servers" that simulation would be running on is far enough to be ignored for all purposes. Those servers have to be there so we go back to the same laws, for any law diverging from the fundamental preservation laws would cause infinite loops that would crash the server immediately. The paradox of the simulation is then that we can't escape reality, even if we are in a simulation. So that can't be a concern. The one fear left is about emotions: how do I know that her love is true? And from the above conclusion we arrive to: regardless of the layer of reality you're in, you can't know, not even assuming the simulation is the only layer.