The first patent laws existed in 500 bc - http://en.wikipedia.org/wiki/Patent#History. Henry Ford did not invent the car. His innovation was to give his company a competitive advantage via the use of the production line. He was therefore able to produce cars faster and more cheaply than his competitors. For the example I used, with the pharmaceutical, this doesn't particularly apply. The innovation is in the product itself - any company can make it once its been discovered, but the discovering company will be at a disadvantage due to massive research debts - hence the need for a patent. (And the benefit to society is a) companies continue to invest in researching new drugs and b) they disclose their research and, after a period of time, it becomes public domain.)
I think you also misunderstand the (intended) purpose of patents. They're not for patenting an application per se. ("the car") but a specific innovation (e.g. some specific of how a part of the engine works). This is hugely beneficial to the general populace because I can come along and build cars too, but I have to think up something that replaces the component that would violate the patent AND give me a good selling point for my cars over his.
I can't even reverse engineer some sort of control, because it is patented. That means that I can't write the best app and prevents me from competing.
See what I said above about the situations in which patents should be used. The software industry in particular (although not only them) have been using patents to suppress competition, rather than protect innovation. Patents are mostly not suitable in this case - but that doesn't mean patents are not suitable in other circumstances.