How does a Christian justify free thinking? What types of Christianity promote free thinking or thinking for yourself?

The more I go to church, the more I feel guilty for free thinking and feel I should be passive to let the Holy Spirit guide me (but I find it is the will of other men that becomes bigger).

So what does Christianity say about free thinking? 
How and when are we not supposed to think freely?

EDIT
What if after deep prayer and meditation and critical thinking, my interpretation of a Biblical concept is different than the logical understanding of it, held by the majority \?
Thinking is actually commendable and encouraged for Christians.  

In Thessalonica, Paul's witness is recorded as follows:

And Paul went in, as was his custom, and on three Sabbath days he reasoned with them from the Scriptures, 3  explaining and proving that it was necessary for the Christ to suffer and to rise from the dead, and saying, “This Jesus, whom I proclaim to you, is the Christ.”  Acts 17:2-3

So, Paul's method was to reason and logically demonstrate the truthfulness of the Gospel.

After Thessalonica Paul traveled to Berea, who were commended by Luke as follows:


  Now these Jews were more noble than those in Thessalonica; they
  received the word with all eagerness, examining the Scriptures daily
  to see if these things were so.  Acts 17:11 ESV


The Bereans were commended for doing their research, considering what Paul was saying, and searching the Scriptures to verify the truthfulness of Paul's claims.  So, thinking was commended.

Throughout Scripture, God asks us to think, to consider, to contemplate.  Proverbs is full of exhortations to the many who makes wise decisions.  I have heard that the book of Romans apparently used to be used in Law Schools in America to demonstrate how to construct a logical argument.  

Christianity proclaims itself as a logical, rational, convincing truth.  It invites the skeptic, the critic, and the scoffer to ponder.  Many of such people have done so and come to faith in Christ, notably Josh McDowell and Lee Strobel, among many others.