Religious tolerance and freedoms do come out from holly scriptures of any religion, they are stated in Koran and in Bible nearly in the same way: "avoid unfaithful" not persecute them but simply avoid. These words have a deep meaning, which refers not just to the religion but also to any other belief and views. Roger Williams was the first minister who introduced the principles of modern religious liberties into the civil practice as he wrote in the Bloudy Tenet of Persecution (1640):
No man shall be required to worship or maintain a worship against his will." Until then, Europe and America had endured what Thomas Paine later called, "the adulterous connection between church and state."
In order to defend the representatives of different confessions and guarantee free participation of citizens in country's public life, there had to be taken measures that would preserve from the dominance of one religious confession over another and from inclusion of religious authorities into government from spreading their influence and dominance there were taken measures that made all confessions equal in rights by separating church from state forever.
James Madison argued about the importance of protecting citizens' religious beliefs, as religion was one of unalienable rights of people that were protected and guaranteed:
that Religion or the duty which we owe to our Creator and the manner of discharging it, can be directed only by reason and conviction, not by force or violence." [Virginia Declaration of Rights, art. 16] the Religion then of every man must be left to the conviction and conscience of every man; and it is the right of every man to exercise it as these may dictate. This right is in its nature an unalienable right. It is unalienable, because the opinions of men, depending only on the evidence contemplated by their own minds cannot follow the dictates of other men"...(Madison, James Memorial and Remonstrance against Religious Assessments 20 June 1785)
Legislature that was issued after the American Revolution had opened a new era in society' relations with church as the U.S.A. had become the first state were religion was officially separated from state:
The amendment stands in these words: "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof, or abridging the freedom of speech or of the press; or the right of the people peaceably to assemble and to petition the Government for a redress of grievances."
To these observations one fact will be added, which demonstrates that the common law cannot be admitted as the universal expositor of American terms, which may be the same with those contained in that law. The freedom of conscience and of religion are found in the same instruments which assert the freedom of the press. It will never be admitted that the meaning of the former, in the common law of England, is to limit their meaning in the United States." (James Madison, Report on the Virginia Resolutions)
Other fathers of American constitution argued about the questions of church and state as well, as it referred to the general concept of human liberties. Thomas Jefferson in the letter to Danbury Baptist Association of Connecticut on 1802-JAN-1 wrote:
contemplate with solemn reverence that act of the whole American people which declared that their legislature should 'make no law respecting an establishment of religion, or prohibiting the free exercise thereof,' thus building a wall of separation between Church and State..."
Moreover for James Madison the question about separation of church from state and secularization of society was one of the questions of main importance:
Strongly guarded as is the separation between religion and Government in the Constitution of the United States, the danger of encroachment by Ecclesiastical Bodies may be illustrated by precedents already furnished in their short history."
Arguments about the role of church in public life of society continue and nowadays, as the influence of religious authorities over some public questions is quite big and officials have to take it into consideration when making decisions. But the principles that laid into the fundamentals of the state's sovereignty had resulted not only positive feedbacks from people, but trust to the government and further immigration of religious refugees all over the world, who found the freedom of conscience in the U.S.A. And religious independence.
The relations of church and state were developing in different ways but the main focus was directed on saving church's autonomy and creating of adequate conditions for its existence, in order to satisfy people's moral and conscience needs.
Since Jackson's presidency there was established a law that gave the freedom to religious organizations that were acting on the territory of the country. Everyone was free from the church taxes, and churches were free as well in their activities and property issues. As a result there were no religious conflicts, that were typical in European countries and all religious congregations could freely develop without any restrictions from the face of the state. It later shaped the religious diversity that became a common thing in the country, one more time showing that the human inalienable rights in freedom of religion choice were observed.
The diversity of religious confessions and their liberties in comparison with conservative societies of Europe, made church more accessible for different people and turned it to be one of the integral components of modern American culture. Even in the epoch of different social revolutions the need to refer to the eternal moral values exists and does not decline, once again showing the importance of morality and human dignity. Confessional membership also reflects the level of civil consciousness and morality; as such kind of society is more obedient to laws.
To my point-of-view in the secular states there are no serious contradictions and discords between church and state: the situation of church in the state is stabilized and is not subjected to some sort of serious changes. Probably it's achieved by the mutual work of state institutions and church, with the results that satisfy both sides. But to my point-of-view state has a great potential to have influence on church's situation by means of accepting laws that would be mandatory for execution. It has to be realized in order to prevent the cases when church will try to expend its powers over the legal limits, so that these laws will make all its claims reasonable. The nature of the restrictions may have a very specific character: for example issues that refer to the commercial and business activities of church. These measures would prevent any feedbacks from the side of confession members, as church probably won't use congregation members in order to defend its interests. At the same time there are lots of issues nowadays that have to be seriously revised as tey refer to the influence of church on state, on its functions, laws and norms. It has a direct reference to the question of education, especially public school education. One of the examples may be the claims of some religious authorities in some particular states to prohibit studying of evolution theory according to Darwin, as it contradicts the religious principles of creation even though that Catholic Church agreed on "creation through evolution."
That's why we have to take into consideration the degree of influence, which church has on religious people, and it doesn't matter what kind of state is it: secular or theocratic.
Nowadays one of the problems that has a global international character is the problem of aggressive religious trends. As the most dangerous tendency for international security is Muslim fundamentalism. Religious fanatics had caused a lot of misfortune, grief, broken lives and broken destinies as well as numerous victims. The only mean to assert their views and beliefs they have chosen to be military resistance, realization of cruel and inhuman tactics of terrorist acts, causing the victims of guiltless people and what is most terrible causing child victims. Generally understood that it's impossible to achieve anything by such bloody means and serious measures have to taken in order to exterminate this evil.
I think that evolution of relations between state and church still continues. The exploration of this theme doesn't loose the actuality nowadays, and there are a lot of premises to consider that philosophers and scientists won't neglect studying relations of these two institutions, opening and explaining new questions of their interaction, and mutual influence.
Madison, James Memorial and Remonstrance against Religious Assessments 20 June 1785
James Madison, Report on the Virginia Resolutions
Roger Williams the Bloudy Tenet of Persecution 1640;
Ward, Nathaniel the Simple Cobbler of Aggawam, 1645