Software is an implementation of an abstract process; implementations have a copyright, processes can have a patent. It works this way for every patentable subject matter, not just algorithm patents and similar.

If I design a new process for synthesizing a chemical, I can patent it. The patent does not describe the implementation, only the abstract process. A chemical engineer may design an implementation of that process, which is protected by copyright. Similarly, an algorithm (which is a process) may be patented but there may be several implementations of that algorithm that have a copyright.

There is an unfortunate myth that an implementation of a patented process being protected by copyright is unique to software. It most certainly isn't. In the chemical process patent area it is quite common to license a patent from one party and license a copyright for an implementation from another. In fact, this is generally how all patents work.