Switzerland is a multi-lingual country, with four official languages: German, French, Italian and Rumantsch. To be absolutetly formal Switzerland is a confederation of states (a.k.a. cantons) and its formal name is Helvetic Confederation.

So when time came for a country code, the latin version "Confoederatio Helvetica" has been chosen.

Note that people from the french-speaking part will argue that CH comes from the french "Confédération Helvétique".

More about it on www.about.ch