As preppers, we aren't planning for the literal end of the world, but surviving disasters. Even the subject of this blog, the tribulations and second coming, is not about the end of the world. Other people do think of ways civilization, the world, or the universe will end. And thus, this article from the Guardian about possible ways humanity may be snuffed out. (Of course, coming from the Guardian, the author cannot help but throw in a few anti-religious jabs).
Interestingly, amongst the various possible catastrophes--including a few based on quantum physics--there is no mention of pestilence. Considering that most of the deadly infectious diseases we know about appeared less than 2000 years ago, and some have had lethality rates of 50% or more, I would think that the possibility of some new disease appearing, for all intents and purposes, out of nowhere would rate at least a mention.
I've written before about the Black Plague, and recently finished an interesting book called Germs, Genes, & Civilization by David P. Clark, discussing the impact of infectious diseases on key events and trends in history. I think that this is a very real threat. In that regard, you may want to look at this recent story about researchers that have developed a more contagious version of the bird flu.