According to an urban legend:
Urban legend says that when airline names were awarded -- I believe in 1946/46 -- the Czechoslovak delegation, not versed too much in English, just said OK to the questions asked. So the name stuck.
I do not much believe in the legend, but still the question remains.
I would expect that at the time when the (then) Czechoslovak Airlines were assigned the code, there were not so many airline operators as nowadays and that
CS (or something similar) must have been available.