Because the sound of X in English is that of a vowel sound. What this means is that you pronounce it "EX", with the sound of the "E" first. Ergo, one says an "ex". It's actually logical in this case...
The X is not an abbreviation of another word. X-Radiation is a form of electromagnetic Radiation having a wavelength of 0.01 to 10 nometers. In other languages XRays may be called Rontgen Radiation...