Of course software patents and other bad digital property rights schemes stifle creativity -- there's simply no incentive to innovate when it's easier to extort.
The bigger problem is that the law hasn't kept up with new kinds of property and most property rights laws, like patents and copyrights, were designed for the physical world and meant to apply to things like mechanical parts and books. They simply don't translate to new, different types of digital property, and consumers and innovators are left with weird, backwards rules.
Fortunately, I don't think the system needs to be completely overhauled. Voluntary schemes like Creative Commons are excellent solutions to some of the problems -- and they don't require new laws or government intervention at all.