Whenever I run into this kind of question in the general public, I am not surprised. Most people have no idea what liberty means, or of the principles behind it.
When I receive this kind of question from posters on Free Republic, I am absolutely amazed. These are supposedly people who love liberty and the principles this country was founded on, yet this question is answered in every piece of literature written by the founders of this country.
First, let me say, as a class, atheist are no more clear headed about these things than any other class and there are just many stupid bad atheists are there are stupid bad anything else. That is why I specified "thnking atheist," as opposed to the run-of-the-mill kind.
There are two answers to you question, one short, one long. I will spare you the long one in detail, because you can figure it out for yourself.
But first we have to say what we mean by, "free to think," because it is obvious everyone is always free to think whatever they want. There is no way to force someone to not think something. What we really mean by, "free to think," is freedom to put one's thoughts into action. In a Muslim country you are as free to think as you are anywhere else, but if you think there is no Allah, you better not say so, and if you are a woman and think there is nothing wrong with showing you bare legs, you better not put your thoughts into action.
Now the short answer is, if (1) the principle is accepted, that it is right to restrict some people's thinking (acting on what they think), there is always the danger, the people whose thoughts will be restricted will be one's own, but if (2) the principle is accepted, that it is wrong to restrict anyone's thinking, the freedom of one's own thoughts are guaranteed. The thinking atheist or thinking anyone else will obvious favor principle #2.
The long answer has to do with the principles of social ethics (philosophical politics) and the nature of rights and liberty. The only danger to the freedom of thought is from other people, particularly in the form of government. The desire for the freedom to think (and therefore the freedom to speak and write and act on what one thinks) is only possible within the framework of a political system that guarantees individual liberty for everyone. If you are familiar with the principles the US government is founded on, the rest should be clear to you.
There are two not very long books that provide very clear answers to all these kinds of qeustions. Both are by Ayn Rand: The Virtue of Selfishness, which explicates the principles of rationally derived objective ethics, and Capitalism: The Unknown Ideal which explains the nature of a moral social/economic system.
If you have an aversion to Ayn Rand, as some people do, especially those who have never read her, you can find the these same principles, (less clearly and not as fully explained), in John Locke, whose philosophy the design of our government is based on. He also originated the concepts of, "rational self-interest," (virtue of selfishness) and "the social contract" (a capitalist ideal).
Hank
That's silly if what you're implying is that this state exists any more in atheism than anything else. Christianity is predicated on this. You can choose to follow Christ or rejct Him.