The word taxonomy has two slightly different meanings. Taxonomy is the science of classification, and is always used as a singular word. Taxonomy can also be the description of a specific hierarchical collection of terms or concepts. In this form taxonomy is used for one such collection, whereas taxonomies refers to multiple taxonomy collections.
Some concrete examples might be useful. A collection of teaching subjects might be described as a Subject taxonomy. If there is also a Country taxonomy and a Language taxonomy, in a collection such as a PoolParty instance, then this is a set of taxonomies.