Arguments about religious freedom

Vatican Museum (open source photo)

Exactly what does separation of church and state involve? Keeping religious preferences out of politics? Keeping religious preferences out of government? Keeping religious doctrines out of public moral issues? All of the above? None of the above? And when does it include keeping the government out of religion? 
Right now all religious freedom is being threatened by both state and federal governments forcing churches to offer services that are not in alignment with their teachings. For instance, Catholic social agencies are being forced to either shut their doors or allow same-sex couples to foster or adopt. All feelings about same-sex couples and marriages aside, this is a complete violation of the separation of church and state.
The same thing is happening to Catholic Church owned hospitals- offer abortions and birth control or risk getting shut down! And another instance is the US Conference of Catholic Bishops (USCCB) Office of Migration and Refugee Services was denied federal funding for its highly regarded services that aid trafficking victims, after the Department of Health and Human Services stressed a preference for grantees that provide family-planning services. Did you catch that- a US federal agency prefers to give money to organizations that provide birth control and abortions. 
The current state of federal legislation is to support organizations that represent a more liberal agenda and to penalize organizations and churches that do not. Those who are happy with a more liberal agenda will praise this and call it a good separation of church and state. But really it is the equivalent of reverse affirmative action [where preference for minorities hurts the majority]. We work so hard to keep religious beliefs out of government that the legislation now favors anti-religious behavior and activities. 
I don't agree with this at all. It will be interesting to see if someday the world becomes so jaded against religion, that we completely kill it, before finally coming full circle with it and begin to protect religious liberties again. 


To read the pending legislation regarding religious liberties - 
House Judiciary Committee’s Subcommittee on the Constitution
Protect Life Act (H.R. 358), (recently approved by the House and Senate in a bipartisan vote) (Also read, GOP Abortion bill passes House)
Abortion Non-Discrimination Act (H.R. 361) 
and the Respect for Rights of Conscience Act (H.R. 1179).

Sources:
Bishop Lori to Congress: Respect Religious Freedom

Archbishop Chaput: Religious Freedom Should be an Election Year Issue