RSA is a really clever algorithm. Its creators deserved to make money off it. Principal component analysis, the fast Fourier transform, and MPEG compression are all very clever algorithms whose inventors deserved to have gotten rich off them.
Being able to patent algorithms is a good thing. The problem was the USPTO's standard for obviousness, which was too low, and let people patent stupid stuff like one-click shopping, hyperlinks on cell phones, or email over wireless.
Everybody who posts something against software patents, but does so not from actually knowing anything about software patents, but because they believe that patent, copyright, and all intellectual property is inherently bad, and all software and music should be free, should post a note to that effect so we know they're crazy.