We use the letter X in X-men much the same way the letter X is used in Xmas. Hopefully the following article, in part by R.C. Sproul, will explain both applications:
The X in Christmas is used like the R in R.C. My given name at birth was Robert Charles, although before I was even taken home from the hospital my parents called me by my initials, R.C., and nobody seems to be too scandalized by that.
X can mean so many things. For example, when we want to denote an unknown quantity, we use the symbol X. It can refer to an obscene level of films, something that is X-rated. People seem to express chagrin about seeing Christ’s name dropped and replaced by this symbol for an unknown quantity X. Every year you see the signs and the bumper stickers saying, “Put Christ back into Christmas” as a response to this substitution of the letter X for the name of Christ.
There’s no X in Christmas
First of all, you have to understand that it is not the letter X that is put into Christmas. We see the English letter X there, but actually what it involves is the first letter of the Greek name for Christ. Χρίστος (Christos) is the New Testament Greek for Christ. The first letter of the Greek word Christos is transliterated into our alphabet as an X. That X has come through church history to be a shorthand symbol for the name of Christ (we have many other shorthand abbreviations like the letter theta (θ), which is a shorthand abbreviation for God because it is the first letter of the word θεός (Theos), the Greek word for God.)
X has a long and sacred history
The idea of X as an abbreviation for the name of Christ became popular when the early church used the symbol of the fish as an acronym. Fish in Greek (ἰχθύς- ichthus) involved the use of the first letters for the Greek phrase “Jesus Christ, Son of God, Savior.” So the early Christians would take the first letter of those words and put those letters together to spell the Greek word for fish—χ for Christ. That’s how the symbol of the fish became the universal symbol of Christendom.
As Christians we want to embrace the traditional and sacred symbols of our faith, whether the X or the rainbow, regardless of how the enemy tries to distort them; therefore, we have adopted the use of the X in our X-Men ministry as a matter of identification with Christ.