That was a story - told by Morpheus. He was a superstitious character - and there was no good reason to think that he knew what was actually going on:

That Morpheus has misunderstood what is going on is underscored by his mention in the same speech of the machines' discovery of a new form of nuclear fusion. Evidently, the fusion is the real source of energy that the machines use. So what are humans doing in the power plant? Controlled fusion is a subtle and complex process, requiring constant monitoring and micromanaging. The human brain, on the other hand, is a superb parallel computer. Most likely, the machines are harnessing the spare brainpower of the human race as a colossal distributed processor for controlling the nuclear fusion reactions.

- http://www.kurzweilai.net/meme/frame.html?main=/articles/art0553.html