The Court says:
This decision concerns only the contraceptive mandate and should not be understood to mean that all insurance mandates, that is for blood transfusions or vaccinations, necessarily fail if they conflict with an employer's religious beliefs.Men could need blood transfusions or vaccinations, so of course they can't allow the exemption from Obamacare to extend to them. The Court then says that this ruling is preventing discrimination. That would be discrimination against who really matters to the majority of the Roberts Court—corporations.
The decision also only applies to "closely held" corporations, which the IRS defines as having more than 50 percent of its stock owned by 5 or fewer individuals. It says that the Religious Freedom Restoration Act requires that the "government provide closely-held corporate objectors the same accommodation it already provides nonprofit organization objectors."
So religious belief trumps medical science and women's ability to make their own health care decisions, and corporations get to dictate that, according to the majority of the Supreme Court.