I have never heard of anyone attributing the cross on the Swiss flag as a Christian cross. The shape is not at all similar to that of the traditional Roman or Orthadox crosses. The root might of course be there, but it was designed over 700 years ago, when such attitudes were more common. We keep the same flag out of tradition, and as such we can forgive any such exclusive attitudes, real or imagined, because they do not necessarily reflect today's values. If the Swiss decided to create a new flag today, it would probably be quite different simply to avoid any such slights - real or imagined.
The same goes for other flags which have overt religious symbols on them. If the flag has been around for a long time, I consider those symbols OK
- there is value in tradition and continuity. But if you decide to adopt a new flag, it should reflect the nation's values today and for the foreseeable future. In today's world, a nation that grants priviledges or rights to members of one religion and denies them to others is medieval, and designing a flag today which might be interpretted to embody such discrimination is hardly a step in the right direction. It simply says that they have either not evolved, or at worst, have evolved backwards.
The only thing you should feel when shooting a terrorist: Recoil.