Maybe the machines were spiteful after the humans blotted out the sun? Or maybe the Architect convinced them he could build the perfect simulation for humanity so might as well use them as batteries?

It's a movie based on a war with machines. Like if Skynet won but didn't actually want to kill all the humans. In fact, in the tv show Sarah Conner Chronicles, a liquid metal T1000 goes rogue and decides the only way forward is to find a way to coexist.