Exactly. While JFK and FDR evoked God at particular moments, in the case of FDR in a moment of extreme national crisis, the Bush crowd makes decisions about foreign and domestic policy based on their interpretation of Biblical law. It is the very opposite of seperation of church and state. No one is saying you cannot have faith. As I mentioned earlier, every President has been a Christian, with the exception of Thomas Jefferson who was a Deist. So the issue is not "Christian" the issue is a particular kind of Christianity. Something TSG has said a bunch of times.
Kind of since always. Jews and Catholics had a very rough go of it for the majority of U.S. history and don't get me started on Muslims in the present day (remember how many people voted against JFK because he was Catholic, not Protestant). Americans have demonstrated an open willingness to discriminate based on religion, even if the law of the land says otherwise. This isn't a huge stretch. This country had legal systems of racial discrimination even as it professed to be a place where "all men are created equal." Now if by "acceptable" you mean "legal" well OK. But homosexual sex is "legal" in America, but it is still unacceptable in most places outside of major cities.

But protestant Christians....yeah, they really have never been subject to systematic discrimination in this country. Now is no different.

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Yesterday, John McCain actually said that if he’s president he’ll take on, and I quote, 'the old boys’ network in Washington.' I’m not making this up. This is somebody been in Congress for 26 years, who put seven of the most powerful Washington lobbyists in charge of his campaign. And now he tells us that he’s the one who’s gonna take on the old boys' network,” he said. “In the McCain campaign that’s called a staff meeting!- Obama, 9/17/2008