This is yet another great example of why. For one, you already get a copyright on the software you write, as well as any books or pamphlets that your company might write to describe your business process. So there really is no reason for the patent -- you can use your copyright for all types of business practices.
Second, the purpose of patents was to protect an inventor for a limited time to encourage invention. They required you to turn in a prototype to get one.
I think we need to go to a system where you have to turn in a working prototype of a physical invention to get your non-renewable three year patent.
If you can't turn your prototype profitable in three years, move out of the way so that someone else who can execute better than you can do it instead.