And you don't really hear about that many atheist from the 1st century either. Now I do believe that there may have been one or two people around that didn't "believe" that there was no God but there has never been a time that evolution, matterialism and atheism has had a government, taught in the public schools and survived for very long.
There have been atheists since the beginning of recorded history. The only reason why there has rarely been a complete separation of church and state in the past is simply because the power-hungry political leaders often find the power of religion (or nationalism) very useful; national and religious leaders often work together to secure a tighter control over the power by using religion to enforce their dominance over the people (e.g. the Divine Right of Kings).
Think about pre-revolutionary France; think about modern-day Afghanistan; think about any nation where the clergy had a hand in the government, and corruption and oppression have almost always accompanied them.
So no, there haven't been very many long-lasting governments who allowed freedom of religion and didn't push religious dogma down school children's throats, primarily because it is in the best interest of power-hungry monarchs and clerics to seize power by claiming religious superiority and to take away the rights of those whose religious views differ from their own in order to better control the masses. That said, there have been a whole lot of really despotic theocracies who
have pushed their religious dogma in public schools or public forums.
The opposite of a theocracy (a government ruled by clerics or religious law) is not necessarily an atheocracy (a government in which religion is illegal). For those who believe in separation of church and state, the opposite of a theocracy is a secular government (one ruled by laws, with checks and balances on power, and freedom of religion with religion being a private, not a governmental, matter). Surely you see that countries that have secular governments, such as modern-day Switzerland, Denmark, Canada, Luxembourg, Austria, Belgium, Japan, Iceland, and Australia, are better places to live than theocracies such as Afghanistan, Iran, and Saudi Arabia, don't you?
And don't imagine that only Islamic theocracies have been guilty of oppression and persecution of minority religions. There have been plenty of Christian theocracies that have done the same. The only reason most modern countries with Christian majorities are not as oppressive of religious minorities as they were in the past is because most of their governments have been infused with large doses of secularity in the last 200 or so years. If the
Puritans had been allowed to right the Constitution, rather than deists and rationlists, Baptists, Quakers and other religious minorities would have been wiped off the U.S. map.
Giving power to clerics, priests, or fundamentalist religious majorities almost always leads to oppression, corruption, and downright genocide in some cases. The logical solution to this is to establish a democracy where religion is neither forced down people's throats nor declared illegal, and where religious choice is a private matter, not a public one.
If we as a nation start handing over power to religious leaders, it won't be too long before people of minority religions such as Islam, Hinduism, Buddhism, Mormonism or paganism, will be persecuted. And then once Christianity has established itself as the prevailing religion, we will begin to see power struggles between Catholicism and Protestantism, and then Evangelicals and non-Evangelicals, and then between Southern Baptists and Church of Christ. Are you so sure that
your religious sect will be the one to prevail? Is that a bet you're willing to take at the expense of everyone else's freedom?