A system with a hundred thousand components can use hundreds of techniques that might already be patented. Since each patent search costs thousands of dollars, searching for all the possible points of danger could easily cost over a million. This is far more than the cost of writing the program.
The costs don't stop there. Patent applications are written by lawyers for lawyers. A programmer reading a patent may not believe that his program violates the patent, but a federal court may rule otherwise. It is thus now necessary to involve patent attorneys at every phase of program development.
Yet this only reduces the risk of being sued later--it does not eliminate the risk. So it is necessary to have a reserve of cash for the eventuality of a lawsuit.
When a company spends millions to design a hardware system, and plans to invest tens of millions to manufacture it, an extra million or two to pay for dealing with the patent system might be bearable. However, for the inexpensive programming project, the same extra cost is prohibitive. Individuals and small companies especially cannot afford these costs. Software patents will put an end to software entrepreneurs.