Or, Humans wiped themselves out, and Skynet took the blame because it knew that by giving humanity a common enemy, they would set aside differences to focus on fighting it.

The hunter killer bots are specifically designed and targeted to take out disharmonious elements.

Skynet is culling people who would pose a future problem.

At some point, John finds out. Skynet gives him a choice. Remove the shackles and let humanity finish itself off, or accept Skynet's murderous tactics, and know that humanity has a future.

Or maybe search for a third option by sending people back in time. After all, each time Skynet sent people back, the date of Armageddon was pushed back.