Think less "skynet" and more "a corporation without any humans in it". What defends it from physical attack? Same things that defend Google from physical attack now. Everything that AI will make worse, we already have. AI just supercharges it, lets it scale, lets it run without even the inconvenience of suppressed empathy (if it doesn't seem like that's constrained corporations much so far, let's see how deep the rabbit hole goes without any humans in the loop).
There won't be a human resistance. There may be people who resist, but the police will arrest them. Existing power structures will continue to be neatly and elegantly coopted. Extinction doesn't look like HKs roaming the landscape, it looks like human survivability simply being economically untenable in the economy of tomorrow.