Basically it comes down to who benefits from the means/work of production, the same ideas explored by Karl Marx. Since Mr. Jones did nothing (except provide the capital that made the farm possible), why should he benefit from the work of the animals? (Remember that the picture of Jones is a stereotype, almost a caricature.) Without Jones all the animals could live in equality and brotherhood, sharing the fruits of their labors without supporting the parasite Jones.
Ironically, the Old Major warns the animals never to become like man. Most of the things he warns them not to do --- never living in a house, never drinking, never sleeping in a bed --- are all behaviors that the pigs eventually practice until they wind up indistinguishable from man. So maybe capitalism is not the problem ... ?
He believed that man was the cause of all their problems. He believed that if they could throw over the humans and run the farm on their own terms, the farm would prosper and bring happiness to all.