What happened to the liberty of conscience?

From the Family Institute of Connecticut blog:

I’ve been wondering lately, why is it that people are tending to view religious freedom as something evermore narrow? Is that freedom only for the clergy? Is it only applicable when practiced in a certain building, or upon a certain day and time? Yet as I read the text of the First Amendment, I can find no such limitations. The freedom is guaranteed for all citizens, at all places and times. It is for everyone, 24×7.