The Luftwaffe could have carpet bombed Switzerland's citites. The Swiss didn't have as large an airforce as the English and their country's cities are smaller too. Maybe if all the living dwellings of the Swiss were just a pile of rubble it would have let the German ground forces in their Blitzkrieg take over more easily.
But a waste of time, manpower, and bombs for the Germans. And like Adler said they still had the mountains to fight from. Even if the Germans could manage to establish a Goverment, the Swiss insurgents would have had many places to hide and strike from. Similar to today's wars, I suppose.