For the same reason that "an ontology" can refer to a unique underlying, external reality (even though the word strictly denotes "the study of reality"), "a methodology" can refer to a fixed structure of methods.
The concepts left in the open, then are "collections of ontologies" or "collections of methodologies". And does two methodologies mean anything more than methodology if they are not disjoint?
But what about words like "physics"? By the above logic, the word "physiology" should really mean "the study of physics", right? Well, apparently the word "physic" used to mean "the study of the natural world", of which both matter/energy and biological systems are made. So, at some point, some yahoo (or yahoos) decided to jargonize the words, over-defining them to indicate something peculiar to one discipline. If I had my way, I'd call the people who study the particle zoo and gravity, "physicians"... and their discipline "physiology". And I'd call people who study biological systems "biologists", and their discipline "biology". Of course, that leaves out the more clinical, treatment-oriented people we call "doctors" or "physicians". I think I might call them "applied biologists".
But, to return to the original point, there is no such thing as "an ontology", there is only "ontology", the metaphysical study of the nature of being. So, the next time some XML-weenie uses the phrase "an ontology" or "ontologies", just poke them in the chest, give them an intense look, and walk away.
As for the rampant abuse of the term "methodology", there's not much we can do about that. There are 3 reasons we're stuck with it.
The combination of these 3 realities (I sure hope someone catches that) results in the continual abuse of words like "methodology".
Perhaps one day, I'll have a hypothesis for why so many people, including college graduates and authors (for cryin' out loud), mispronounce the word "nuclear". That one still baffles me.