This applies narrowly to closely held, family owned Corporations. It is not an overturning of the whole contraception mandate, but the Court was not asked to do that in the first place.
The Catholic Church still has their challenges to this as well, and I would look for a lawsuit to work its way up to SCOTUS, perhaps in the next term. This Obamacare mandate battle is not over, and there will be others to come likely for years.