To some, this question may sound bizarre. What? Here in America? Lose our freedom of religion? No way! To others, the question may sound like a “conspiracy theory.” Just calm down, they may say. Don’t get bent out of shape just because of some minor differences of opinion on whether birth control and drugs that abort babies should be freely provided through medical insurance.
If you’ve been watching American trends, you will see two worldviews at odds. A secular naturalist worldview (which includes socialism, humanism, and atheism) diametrically opposes the Biblical worldview. Consider the following: 1) The sanctity of human life has always been defended among people influenced by Biblical thinking, but 30+ years of legalized abortion in the U.S. has changed the way we view human life – in or out of the womb; 2) Faithful marriage between one man and one woman has always been supported by any people influenced by Biblical thinking, but U.S. courts are now ruling in favor of so-called “same-sex marriage;” 3) Freedom of religion is the first freedom enshrined in the Bill of Rights written by Founding Fathers influenced by Biblical thinking, but today we are told that “sexual freedom trumps religious freedom” and that while we may have freedom to “worship” (a private practice), we shouldn’t publicly practice our faith during the course of our everyday lives.
Are we in danger of losing the right to practice what we believe to be true? Think about it. 1) Religious organizations who believe abortion does not please God have been told their health insurance providers must cover contraceptive use (including drugs known to end the life of a baby before birth) and, therefore, go against their faith and conscience; 2) States like Iowa where the majority of citizens do not believe in “same-sex marriage” must recognize the “right” of two women or two men to “marry” and, in states like California, the majority vote in favor of traditional marriage was overturned by a judge in favor of “gay marriage;” 3) Parents who believe that children are entrusted to them by God are being told to obey the “state” and let schools teach students that homosexuality and “gay marriage” are “normal” and, if anyone speaks otherwise, they may be guilty of “hate speech.” Are all of these things – and more – indicative that our religious liberties are being removed?
Followers of Jesus Christ have always – and will always – be different from the world. But, in order to “fit in” with the world, have Christians been silent? Compromised faith? Stopped putting their faith into practice?
Atheists, humanists, and secularists all have a faith, too. It is faith in something other than the God “I Am;” in the Savior of the world, Jesus Christ. They are passionate about their faith. They practice their faith wherever they are: in the schools, media, workplace, courts of law, and places within government. Are Christians less passionate about their faith? Or, have we believed the lie that “your faith is a private matter between you and God”? Jesus said, “Render unto Caesar the things that are Caesar’s, and to God the things that are God’s” (Matt. 22:21). We are to obey government except when it tells us to disobey God. Then, we must speak up and resist evil. We must use God’s Word to defend life, marriage, and family — the very foundation for civil society.
When we are told to keep God’s Word “private” and not share it in the marketplace of ideas, then we have lost our freedom of religion. How, then, can we be “salt and light” (Matt. 5:13-16)?
Recommended resources include Breakpoint, Family Research Council,
World magazine, and Concerned Women for America
Ezerwoman's Blog 
I have been considering this very question in recent months as I’ve seen these things transpire. I also recently picked up Foxe’s Book of Martyrs and have begun reading that. My knowledge of Christian History around the world has been that when the Church is persecuted, it does not fall away, it does not become dormant, it does not “go quietly into that good night”. At first, we would lose from our congregations those who claim to be Christians but as we are persecuted, jailed, fined perhaps even killed (martyred) for our faith, we will become stronger. Sadly, I believe that we have gotten here by 2 routes: 1, as you mention, we have been silent. 2, the Bible says they will in John 13:35, “By this all men will know that you are my disciples, if you love one another.” The homosexual community is being told that “God Hates Fags” and that they will “burn in hell”. they are not being won because we are not loving them. So, they see us going to church, they hear our songs talking about how we love God, how He loves us and how that means we should love our neighbors as ourselves and then they see us doing the exact opposite. Christians TOOK OVER Rome even during terrible persecution by loving and caring for people when nobody else would. When there were outbreaks of plague (bubonic, influenza, etc) the people who could leave the area would, even sometimes deserting children or parents & grandparents. When they did so, the Christians would move in to care for the sick and feed the starving and adopting the children. When the outbreak was over and the rest of the people returned, they found that the children they had deserted trusted the Christians, not them.
I consider myself lucky to be part of 2 churches that have a strong sense of family toward all who walk in the door and one of those also has many outreach opportunities like water bottle handouts at the beaches (I live in Florida), we have cookie or donut drop-offs at police & fire stations and things like that. But I know from visiting churches (something I like to do occasionally) that not all churches are affectionate to visitors. An analogy I once heard on the radio is too many churches have gone from Fishers of Men to Keepers of the Fish Tank.