Patents are killing software innovation?

Martin Brampton had an interesting op-ed that showed up on the EFF list today.

The trouble with having thousands of software patents is that small organizations, whether software companies or in-house development shops, will find it increasingly difficult to write new code without infringing on patents. The argument that the new software was invented independently is no defense against a patent-infringement claim.

I distinctly recall similar problems in other industries where patents exist. What were the founders thinking when they wrote the Constitution? Perhaps the warm, fuzzy feeling of making perpetual charitable contributions doesn't motivate enough people to do more than the minimum to survive?