I think you made some claims that require support. For instance, your statement that any invention "deserves protection" is not automatically true. Granting an innovator the right to a monopoly on his/her product is only beneficial to society as a whole if it improves the availability of technologies to more people than not granting these monopolies. Some, such as Lawrence Lessig (http://www.youtube.com/watch?v=7Q25-S7jzgs) have argued that patents stifle innovation and are a detriment to society.
I believe that your question "if you were starting a business that provides a software solution, would you want to be able to protect your solution from competition?" is in the same mode as the following questions:
"If you had one hundred million dollars, would you want to protect it from thieves?"
"If you had control of the oil market, would you want to be able to gouge the consumer for your own profit?"
"If all the world were your unquestioning slaves, would you want to be able to insure they could not escape?"
From the point of view of an 'innovator', patents may seem intuitive, but unless the research shows that they ACT in the way they are INTENDED, they do not deserve the same reverence that we give to physical property with real physical scarcity.
As for your argument that patents are a part of capitalism, consider that the hallmark of capitalism is supposed to be free markets with resulting competition and prices that (due to competition) approach cost for consumers. Patents disrupt competition and in light of this I find your statement unfounded.