There are 3 forms of IP protection: copyright, patents, and trademarks. The crux of the issue is that, for software, copyright protection is too weak and patents are too strong. So called "stupid patents" are a symptom of this issue, but not the cause. Software ideas don't work well under either of these existing protection models. Further, software patents are especially broken since they've deviated from their originally intended purpose of helping fledgling inventors launch their creations without larger firms stealing their work. Now every large firm has an arsenal of allegedly "protective" patents that can be swiftly mobilized to crush upstart competitors. Similarly, patent trolls can sit on the sidelines and exact royalties far beyond the economic value that their inventions contribute. Bluntly, there needs to be a new form of IP protection to deal with this reality -- this isn't to say I have any strong ideas of what this form of protection should be, just that these are the characteristics of the problem.
The same core issue is starting to become apparent in anti-trust law. These laws are inappropriate for tech firms because they don't scale like traditional businesses (how do you deal with an industry with super high HHI but massive barriers to entry and no easy way to split up existing competitors?), but that's a topic for another thread.