Licensing software per unit of computation time or by value of data processed with the software is less common. You can license written material per use, especially when the documents are in a proprietary electronic format. Customers sometimes look askance at these ideas simply because they are less common. They are suitable for some situations, such as high-powered engineering computation using techniques proprietary to the developer. Intellectual Property Copyright law protects the expression of an idea, such as source code or an article.
Patents protect the idea itself.
You may reimplement a product without infringing on a copyright. You can infringe a patent, even if you've implemented an algorithm from scratch, without having heard of it. Patents are potentially big trouble for small software shops, because a proper patent search costs more than you are likely to make. Trade secrets form a large part of the software world. You will often be asked to sign a nondisclosure agreement before working for a customer.