The ability to think and reason has been given to us by God because we are made in his image and likeness. This is not an end in itself by the mean whereby we can arrive at the truth, the good and the beautiful. And what is truth? Truth is the conformity of of the human mind with the reality God has created. This does not come easily to us because it requires critical thinking and dependence on truth others convey to us. It depends on what we have been taught, the books we have read, etc. In other words the truths we hold have been given to us because it is impossible for each individual human being to discover these truths by himself or herself. In our pride we may say, "I refuse to be made a slave to old traditions and outdated ideas," they say. "I am an original thinker. I think for myself. "I will show what a false statement that is. Apart from the freedom Christ gives, this is nothing but shallow boasting. Your ideas about life and religion did not come from your "freedom of thought" at all. Your ideas came from your parents. Your friends at school and college, your teachers and professors - all these contributed greatly to what you think, about what you call "freedom of thought." Have you ever noticed also that people's views and opinions change as their circumstances change? And yet they boast that they are free! You can say whatever you like but you cannot think what you like. You are bound up hand and foot by prejudices and heredity and environmental influences. You are literally enslaved by those factors which have made you who you are." (Sermon by Dr. R. L. Hymer, Jr. "No Freedom Accept in Christ)
"Freedom of thought" in the western culture has has come about slowly and with difficulty. Socrates and Christ were put to death because their teachings about God we different than those held by the Greeks and Jews respectively.
In the Catholic Church we have seen the period of the Inquisition. The Protestants substituted the authority of the Pope with that of the Bible. Its founders claimed for themselves "freedom of thought" but when people disagreed with them, they became intolerant. As a consequence there are many religious denominations.
With Galileo began the age of Science. The Church made the mistake to interpret the creation story of Genesis literally. Galileo insisted that the sun was at the center of the solar system and since then astronomy has revealed a fantastic universe.
Then came the age of reason in the 17th-18th Centuries which developed primarily in England, France and the United States. Deists for example, raised reason above authority and revelation and in the process sought to create a natural religion. Yes, they maintained, God created the universe but he does not intervene in the processes of natural laws. Therefore, there are no miracles. "What organized religions see as divine revelation and holy books, most deists see as interpretations made by other humans, rather than as authoritative sources." (Wikipedia: Deism) In the 19th century Darwin propose the theory of evolution in which the emergence of life on the planet was seen as the work blind chance. God the designer of all things was banished from view.
Truth is arrived at in two ways: by reason and revelation. The individual by himself is free to think what he wishes but to arrive at truth means employing critical thinking. The idea of reason alone without revelation and the divine authority established by Christ cannot bring us to ultimate truth and freedom of thought has given rise to many errors in the history of Western Civilization. Yes, you are free to think as you like but is what you are thinking true?