Within the EU, there is complete freedom for EU AOC holders as regards routes. This has been so since about the 1990s, when the EU introduced the "Package 3" of regulatory reform and abolished the need for route licences within the EU for EU-based operators.
However, for your specific question: Switzerland is not an EU country. I am unsure whether the Swiss chose to join Package 3: if they did not, then you pesumably still need a route licence to operate between any Swiss airport and any EU destination, regardless of state of registry.