T2 is an exception not the rule, and even then Skynet is still the primary antagonist in that film, the T-800 Model was only protecting John Connor because Connor from the reality where humanity won in the 21st century reprogrammed the T-800 specifically to defend the child version of himself from the T-1000. Yes, child Connor and the T-800 formed a close and tight knit relationship but it was only because a human changed it’s ways forcefully prior to sending it back in time, left to it’s own devices sans adult John Connor it would have been as malevolent as any other T-800 Model Skynet made.