Free thought can be a very dangerous thing. The less informed and the more superstitious any given tribe (any group or groups of people), is, the free thought of one member or group of members can be dangerous to himself and others. When great thinkers with giant brass balls came up with an outside the box ideas, some kind of great happening occurs, usually involving lots of suffering and many times war.
If one lives in a region where it is religious then it can be said that the atheist is the free thinker and vice versa. The greater the threat to be ridiculed and persecuted for an idea, the greater the need for free thought. If it were not the case then we would all be following a more ancient religion or belief system full of ignorance and superstition. Right now in many parts of the middle east, anyone who is not Muslim is in extreme danger, including the atheist. Yet, what is required the most to make it a more peaceful place? The need for free thought, of course.
So, it is your free thought that gets you into trouble, but at the same time it is the only thing that can save you. Free thought is also the most creative and powerful resource we possess. If it is suppressed by fear of ridicule, most people buckle under. That is the case here in the west, imagine being in the middle east and knowing you will be killed if you have a free thought. Kind of makes me feel small thinking of how many times I held my tongue as a young man in school just because someone might make fun of me. Even today, to keep the peace at home, I can't say certain things without people becoming very angry.
How can I associate free thought to the existence of God? Hard to without at least some faith and to those without it, I can't. However, the idea of a supernatural being out there who holds all the purse strings is a great free thought that many people have. It's free in the sense that you can do it outside or inside a religious belief system of your choosing in most of the free world. You can even willingly with free thought totally dismiss it. The people who choose to just go along with what ever the current brand is are not free thinkers or those who ridicule other's free thoughts with malice, they are not free thinkers, they are suppressors or in some cases, like in China and the previous USSR, destroyers of free thought.
To suppress the idea of the existence of God, destroys free thought because God can be many things as well as all things. The atheist who has actually put some thought into it for their own self growth without hatred or ridicule for those who might think differently are free thinkers, but I think they are probably rare. It's hard for us humans not to ridicule others for even the smallest of controversy.
The scientist, the true creative scientist, not stamp collector, is in an awkward spot these days because to answer questions and solve problems they must take leaps of faith. Just like a religious person must to fill a need in their being. But for a scientist to say God does not exist because there is no evidence, well that would make him a pretty big hypocrite. So for those to say,"I live my life based on scientific findings", is one who is not capable of free thought or at least one who will either hold back the tribe or add nothing to it.