RE your first point, you're sort of correct. Courts can award treble damages for willful and wanton infringement of a patent. Courts don't award treble damages willy nilly; they seem to award them when you intentionally rip off somebody's patent. Even if you know of another's patent rights, if you have a good faith claim as to why/how your patent doesn't infringe, and if you have a solid opinion letter from counsel, you generally won't get hit with increased damages, even if you lose the underlying suit.

RE software, I'd tend to agree with you. The original post makes the case that all patents are bad though, and that they specifically prevent that transmittal of knowledge. That's really what I was responding to.