What was the origin of religious tolerance in Europe?

Not sure about reference, but I have read that Frederick II of Prussia was one of the first rulers who believed in religious tolerance.

What you mean is not humanism by any definition. One can call it tolerance or pluralism.

In ancient, polytheistic world it was quite common: people tended to believe that all deities worshiped by other peoples also existed. They were seen either as local deities or just other names for the already known deities.

It was the spread of Abrahamic religions that required the people to struggle for the glory of a single god and to punish those who diverged from that line.

So as far as influence of Christianity reduced, the tolerance returned back, naturally.

Wikipedia has an excellent overview of the history of religious tolerance from antiquity to the modern day. (Unfortunately, it seems to have been ham-handedly shoe-horned into the entry for Tolerance, which is a political science thing unto itself. Gotta love the never-ending Wiki edit wars...)

Here is another, under the heading of "Christian Debate on Persecution and Toleration." It's got a lot of other links on persecution and tolerance with regards to European history.

I'm not even attempting to answer the whole question, just want to give example of a country which managed to avoid the bloody religious wars of Germany or France ( other answer implies that it was the only way to reach religious tolerance ). That country was Polish - Lithuanian Commonwealth, which spanned a large chunk of Europe, and was mostly Catholic, with its kings being exclusively Catholic.

The first codified example of tolerance in the kingdom of Poland was the Statue of Kalisz, announced in 1264. It not only guaranteed Jews the freedom to practice their religion, it actually went much further – one sample paragraph:

Should a Jew be taken to court, not only a Christian must testify against him, but also a Jew, in order for the case to be considered valid.

The statue was later confirmed by kings of Polish – Lithuanian Commonwealth.

In the next century, tolerance guarantees were given to Orthodox Christians, Armenians, and Muslim Tatars.

In 1525 Polish king agreed to a plan of establishing formerly Catholic Duchy of Prussia as his Lutheran fief.

In the XVI century protestant ideas gained supporters in Polish-Lithuanian Commonwealth proper. As a result in 1573 Polish parliament passed Warsaw Confederation act, which gave the protestant denominations the same rights as Catholics. From now on, every newly elected Polish king had to accept those provisions.

So, Poland avoided religious wars of Germany. Another result was that Polish – Lithuanian Commonwealth became attractive destination for “heretics” from other countries, primarily from Germany. It also harbored the biggest Jewish population in the world, and the most orthodox versions of Judaism developed there.

I don't find any particular reason for the direction that Poland (it's kings, gentry and clergy) went regarding religious tolerance, except from pure pragmatism.

But it's just an example country, perhaps someone with more knowledge will comment on the situation in Ottoman Empire and other European states.

Europe gained limited religious tolerance by fire blood murder starvation war and rape.

The guarantee of religious tolerance is cuius regio eius religio: that the nature of the person of the sovereign dictates the religion of the sovereign's realm. Between princes, religious toleration was obligatory due to violence.

Firstly in the Peace of Augsburg (1555), then in the Peace of Westphalia (1648) which guaranteed this principle.

The violence of princes to one another, and the recognition amongst the ruling classes of Europe that continued contestation only opened the way for radical peasants movements and anabaptism, ensured at the end that the religion of princes would be subject to toleration.

Generalised toleration amongst the population came far later, in capitalism, but the link between humanism which brought forth the issue of religious toleration between princes due to the choice of some princes to contest the power of the Church of Rome outside of that Church and find their own salvation, is the link between humanism and toleration. A link forged in the large scale depopulation by violence of many areas of Europe.

(sources: Wikipedia articles on the principle nouns, Blisset's Q, Engels' GPW)