That's strange, I thought X was used to identify pornographic material. Oops, did I just say that?
Seriously, Daniel J is right. A long time ago, mathematicians decided to use x as the primary unknown in equations. They do use other letters, all which have specific meanings, depending on the topic in question.
It may also have something to do with our obsession to abbreviate things. You used the word "unknown", but a more appropriate word is "unexplained." Notice the emphasis on X. un X plained? Does that, prehaps, X plain it?