The First Amendment ensures our freedom OF religion, not your freedom FROM religion.
It's purpose was to restrain government from demanding everyone be Methodist or Congregationalist or Baptist or Catholic or Presbyterian or Jewish or atheist.
It does not give any one group or the government on their behalf, the right to enforce any dogma or prohibitions.
If my religion tells me it is a sin to provide birth control, neither you or the government have the right to demand I do.
By the same token, if your religion or lack of one, tells you that it is ethical and proper to provide coverage for birth control, abortion and sex change surgery, neither I or the government have the right to prohibit you from doing so.
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof
A university choosing not to provide insurance coverage for something it deems is against the rules of its God, in no way establishes a State religion or forces you to be Catholic.
BUT, forcing them to provide such coverage, does prohibit the free exercise of their religious beliefs.