What's wrong with copyrighting work so someone can't just steal your entire source-code and call it their own? Just like you can copyright a book so nobody can steal that exact instance of your thought process but people can still write very similar books.
JRR did not patent 'the application of height-challenged individuals manually transported to a heated device for the purpose of destroying small amounts of jewelery', but the work is copyrighted so you cannot just find/replace the story so it reads Shrodo and Hamwise going to Mt Foomp with their trusty sidekick Bandalf.
To take a quote from your source: "Every writer owes a similar debt to those who have come before." - this is something I believe speaks more to the core of software development than the patent system we use today.
Terry Brooks' supposed imitation of The Lord of The Rings didn't stop it from generating hundreds of millions of dollars in revenue.
I actually support the idea that Terry Brooks should be able to reskin The Lord of the Rings if he feels like it. I bridle a bit at the label "supposed imitation", though. Read them both -- they're exact copies. Even those parts of LotR that are utterly irrelevant to anything are faithfully duplicated in Sword of Shannara.
JRR did not patent 'the application of height-challenged individuals manually transported to a heated device for the purpose of destroying small amounts of jewelery', but the work is copyrighted so you cannot just find/replace the story so it reads Shrodo and Hamwise going to Mt Foomp with their trusty sidekick Bandalf.