This post on Techdirt does a great job of summarizing the problem with patents:
The patent system isn't designed to "protect the little guy." It's designed to promote innovation -- and that's what it needs to be judged on. Patents may make some sense in cases where a concept is truly unique and non-obvious -- but if others are coming up with the idea independently and are better able to bring it to market, then the patent holder is holding back innovation. The other companies didn't "steal" the idea, because they came up with it independently (suggesting that it wasn't unique enough to deserve patent protection anyway).
Note that the post is actually about patents in general, but I'm specifically interested in software patents. If the patent system is in place to enourage innovation, it's failing miserably.
If someone can come up with a system for software patents that truly encourages innovation, I'd like to hear about it. What we have now, a system that stifles innovation at every turn, and where the patent application volume overwhelms the patent office, needs to be dealt with.