Yes, disease can be a problem. But even the most virulent of plagues rarely has a death rate exceeding about 75%. Even if you postulate a 90% mortality rate, with a current world population of about 8 billion people the survivors would still number around 800 million! Hardly a wipe out! Of course, they would be spread out across the globe and civilization as we know it would probably be destroyed, or at least set back quite a ways. But with that many survivors, and with all of the accumulated knowledge of humanity still available, recovery would be steady, if not necessarily rapid.
In fact, ANY kind of major catastrophe, other than the complete destruction of the planet or the destruction of the Sun, would invariably leave survivors, and in generally large numbers. Some of them, like nuclear holocaust or plague, would also have significant impacts on other species. But over all, the biggest threat is to our way of life, our civilization. And even then it's mostly a matter of a change in how we must live rather than complete destruction.