An interesting scenario could unfold from this.
The court ruled that hobby lobby doesn't have to pay for the contraception because it violates their religious beliefs. The employees don't have to pay either, a third party insurer does, and the government can be asked to subsidize this.
Now if this precedent gets lent to someone whose religion is against all modern medicine, the third party insurer would have to pay all the benefits, and can ask the government for subsidies, which would have to be provided lest every insurer in the country go bankrupt in weeks.
That would mean the government is paying all the medical bills, which they would pay for through taxes.
Welcome to government healthcare.