Unlike copyright, patents can block independent creations. Software patents can render software copyright useless. One copyrighted work can be covered by hundreds of patents of which the author doesn't even know but for whose infringement he and his users can be sued. Some of these patents may be impossible to work around, because they are broad or because they are part of communication standards.
Evidence from economic studies shows that software patents have lead to a decrease in R&D spending.
Advances in software are advances in abstraction. While traditional patents were for concrete and physical inventions, software patents cover ideas. Instead of patenting a specific mousetrap, you patent any "means of trapping mammals" or means of trapping data in an emulated environment. The fact that the universal logic device called "computer" is used for this does not constitute a limitation. When software is patentable, anything is patentable.
In most countries, software has, like mathematics and other abstract subject matter, been explicitely considered to be outside the scope of patentable inventions. However these rules were broken one or another way. The patent system has gone out of control. A closed community of patent lawyers is creating, breaking and rewriting its own rules without much supervision from the outside.