The White House administration, the president and his various officials, as well as the media sources whom they favor, no longer speak of "freedom of religion". Instead, they use the term "freedom of worship". It's an interesting choice, for not only is religious freedom plainly stated in the Constitution's amendments, but because there is a difference between "religion" and "worship".
Worship is that done in a limited time frame and generally behind closed doors in a place set apart for such activity, be it a church, mosque, synagogue, or temple. Worship is an extension of faith, the actual practice of renewing the tenets of one's religion and its story.
Religion is, to put it flatly, the basis of one's entire life; our choices and practices. Worship is a tool of religion, but religion is the transformative experience that infuses our existence.
When a government sees religion as mere worship, it is not recognizing the chief feature of this particular freedom. It's as if the government is telling us that they will be supportive as long as we practice our oddities behind closed doors and for an hour or so a week. If we expect to permit religion to serve as the source of our world view, that may be officially less supportable.
Certainly, some of the legal efforts being advanced through the Affordable Care Act make that official perspective seem apparent.
Now, to really complicate the matter, I don't view Christianity as a religion. Instead, I see it as a culture, but that's a whole other discussion.