The warm and fuzzy world peace future envisioned by a dreamer is NOT your future, so get over it.
I can see Big Brother Skynet used to help keep track of terrorists. So it is easy to see it's eventual sentience determined dangerous Humans are BAD. Fact, all Humans can turn BAD so ALL HUMANS ARE A THREAT! Termination is the logical conclusion as unlike machines, Humans cannot be Programmed to behave (YET). The resources to build a CONSTRUCT (A Matrix) to house them and contain their illogical processes and behaviors would be too expensive and untimely. Termination is cost efficent and solves teh problem completely.