X is a quirky letter of the alphabet.
I recently had an interesting interaction with one of my biology students. He had written a laboratory report in which he repeated spelled the plural of "matrix" as "matrixes." Knowing my own mind in these things, I crossed out the first instance of this misspelling and wrote in the margin of his paper, "It's spelled 'matrices.' "
When the student saw my notation, he shook his head slowly and despondently. Then he looked up at me. "I hate the letter X," he said, and it was clear that he wasn't joking.
Well, X is a curious letter, certainly a movable feast as far as pronunciation is concerned. Sometimes it stands its ground, as when some people pronounce it like the name of the letter itself: "X-avier" for "Xavier." At others, it horns in on the perfectly serviceable "ks" or "cs" sound, as in, well, "matrix." It can also be silent, as in the imported word "faux." And it has been known to have Z-envy – "xylophone."
Confusing, yes, but certainly not a reason to dislike it. Language is, after all, a game with many twists and turns. As an example, recall the old saw about the relative positions of "i" and "e": Use "i" before "e" except after "c" or when sounded like "a" as in neighbor or weigh." Great advice, until one bumps up against a word like "protein." Suddenly, the game proceeds in a different direction.
But back to the letter X. Where did it come from, anyway? It seems to be a long story, involving Greeks, Semites, and even Etruscans. Wikipedia says that because it was placed near the end of the Greek alphabet, it was an innovation – I would guess – to clarify some sound that the other letters of the Greek alphabet weren't quite nailing. Be that as it may, the Etruscans borrowed the letter from the Greeks and, before their civilization died out, charitably conveyed it to the Romans. We got it from Latin.