So what's your stance on RSA, one of the early software patents, which is still used everywhere?
I didn't try to articulate every problem with software patents, merely those illustrated by the just-overturned patent covering SSL using RC4. Note that RC4 itself is about 30 years old, and was developed by RSA security.
In any case, regarding the RSA cryptosystem itself, it was developed by several academics (independent of its previous, secret, invention GCHQ), and clearly it would have been developed and published even without the extra bonus of patent protection. It's important to remember that patents are a means to an end ("promot[ion] of Progress of Science and useful Arts") -- which is not to make money for inventors but to provide them an incentive to invent for the public good. In other words, a Patent is a way for the public to give up something (the natural possibility of making use of an invention you hear about) in return for a different advantage (getting the invention made in the first place). If inventors would invent even without the extra incentive, there is not need for the incentive.
Since practically all the value of inventiveness in the software business can be captured simply by writing the software (and, in cryptography especially, by ordinary academic incentives such as promotion, tenure and professional recognition), software patents don't help. Instead they hinder.
For a salient example consider the LZW patent. The algorithm was designed by two academics (Lempel and Ziv of the Technion). The main effect of the patent was to end the widespread use of
PS: It is likely that the LZW patent was invalid (patenting an abstract algorithm), but nobody wanted to take the legal risk of going to course to invalidate it. This obnoxious patent has since expired.