A reason the universe is not "The Matrix"
If the universe in it's entirety was inside a network of computers being simulated then the likelihood is that atoms would have a parent child relationship, where one parent atom would be duplicated from to mimic other atoms of that type in the universe. (Is almost a law of conservation when it comes to programming as one instance of information in memory can be used to duplicate seemingly multiple instances.)
However this would suggest that if there was a bug either the child process or the parent could stop, freeze or die. This would mean that virtual matter in the known universe would have a habit of spontaneously disappearing until some programmer got round to writing a patch.
Quibits
You can suggest that the whole universe is made up of these atoms (and particles) that compute the nature of the universe in both their appearance and their positioning. You could suggest that the whole universe is a giant Quibit (qwib-bit) network and that it's programming and hardware structure are one in the same.
The matrix as a whole was just a genre/story to be sold to the general populous as much as Star Trek, Starwars and Dr. Who are. Some people can have fun imagining their way through those preposed universes, however they are fictional.