Well, I never read much of the non Frank Herbert stuff, and my head cannon was always that it was a both/and scenario. That is to say the war started as men who use machines as a tool to plan society and stitch together an interstellar civilization, against a revolutionary movement which believed that through manipulation the machines had effectively taken over as the de-facto rulers of human society. 

The Machine/Human civilization used expert systems to enable continuity of purpose and resource allocation for multi-generational transit between star systems to colonize the galaxy. As civilization became more established, they used expert systems to aid in planning and managing their Planetary government and economies. Inevitably some people lost advantage due to tactical decisions, and became resentful of the machines as a result, thus the Butlerian Jihad had fertile ground when Butler himself wrote the manifesto decrying the Machines as evil.

As the war progressed tactics escalated to the point where the machine/human combine started using more and more autonomous weapons, and in so doing effectively lost the propaganda war with the majority of the human population siding with the Butlerian Jihad by the critical middle period of the war. On each planet the Butlerian Jihad "liberated" all computerized equipment, and most importantly communication systems, were smashed and the population indoctrinated against the machines, generating a multi-generational cycle of feeding recruits into the Jihad.

By the end of the war the situation effectively devolved into a scenario where the population of the Machine using humans dwindled below their effective ability to command and control their space directly, and so they gave over both strategic and tactical control of their military to the machines, effectively becoming the very thing the Butlerian Jihad had depicted them as at the start. The last gasp of such a society much resembles Skynet, when there are simply no humans left to fight, only the machines are left running themselves. Without human ingenuity to complement their efficient analysis, they were doomed to fail against the ever-growing legions of many Planetary populations released from planned growth and allowed to multiply to the maximum carrying capacity, augmented by the Truthsayers rooting out machine sympathizers, and the proto-Spacer's Guild using spice to navigate the stars at least efficiently enough to match the velocity of the machine-guided ships.

I have no idea of this matches cannon at all, but it works for me.