The way this phrase has taken hold is truly remarkable. But it so perfectly describes so many different circumstances, well beyond the literal storm in the book, and its use as a kind of metaphor for so much else has made it a very effective phrase.
In the book, the perfect storm is a combination of natural elements that converge to create a powerful storm. But there is also an underlying combination of elements that are created by man, hubris being one, the idea that the men have the wit and strength to conquer the elements. These elements also are part of what creates this perfect storm.
Thus, we use this idea as a metaphor to suggest a convergence of circumstances, natural, man-made, or even both, that create a situation of great danger and/or destruction. The term is used for all manner of situations. I have heard it used within the context of the invasion of Iraq, where it has been used to describe the situation in which Iraq imploded into a civil war after the removal of its dictator. I have heard it used to describe the failure of businesses in situations, for example, in which a business recklessly expanded just as the recession hit. I have heard it used to describe the dynamics in a family in which a divorce was imminent. In any context in which we might use the word "storm" as a metaphor, the idea of the perfect storm is a way of heightening the metaphor to show something well beyond an ordinary storm. Of course, it has been overused to such a degree that it is in danger of becoming a cliche, and perhaps it is already considered one by many people.