The compute in the Matrix wasn't handled with human brains. They used the bodies to generate energy, and kept the brains occupied with the simulation so they wouldn't reject the pods.
It doesn't make any sense, of course, because it's a movie.
But hey...if we're going to extrapolate wildly from sci-fi, let's at least know what the stories said.
I think we can all agree that "use humans for raw energy" is a really stupid idea, and sounds exactly like someone dumbed stuff down. FFS, a small Rickover fission reactor the size of a van (1950s tech) produces the same amount of heat as, what, 200 000 human bodies? (And why humans, with all the complex support systems? Why not a heap of compost, if one insists on bio-source?)
Whereas using our brains for compute (in the background, or during REM sleep) makes perfect sense; power efficiency is excellent.
pretty sure the story is that they used human brains as computers
Your statement is correct for the movies, but I think the extended universe (maybe a comic or the original script) did state the humans were used for compute, not energy. It was dumbed down for the films.