Weather stations in North America used to have a two letter abbreviation. When some of those weather stations were outfitted with runways, in Canada they would add a "Y" before the code to mean, "Yes you can land here".

More details: http://www.skygod.com/asstd/abc.html

"X" roughly resembles the Greek letter chi, which is transliterated as "Ch". It's short for "christ". Originally the phonetic value was quite close to the modern English hard "k" sound, which makes more sense for representing "Christ", but chi has actually diverged in Modern Greek to be more like the "h" in "human".