The Constitution barred the federal government from establishing a church. Many of the states did have established churches or state-funded churches. Massachusetts stopped funding the Congregationalist church in 1833. The Anglican/Episcopal church was the established church of Virginia until 1786 (Edited: I had put in 1830, which was the year that state support was ended. The church was disestablished earlier. Thanks to /u/WARitter for the correction). There was a distinction between established churches and toleration as well, particularly among Protestants. There were also state religious tests. New Hampshire and North Carolina required officeholders to be Protestants. The drafters of the Constitution did not want the establishment of a federal church, but they were not necessarily opposed to state establishment and state funding of churches.

Indeed, it was not until the incorporation of the Establishment Clause in the 1st Amendment against the states through the judicial doctrine of incorporation under the 14th Amendment in the 1943 case of Murdock v. Pennsylvania and the 1947 case of Everson v. Board of Education that states were forbidden from establishing a church. Both of those cases, in particular Everson, actually discuss the history of established churches in obiter dicta and provide an interesting look into the historical interpretation of the Establishment Clause and jurisprudence on freedom of religion.

Sources: Everson v. Board of Education of the Township of Ewing et al. 331 U.S. 1 (1947)

Library of Congress, https://www.loc.gov/exhibits/religion/rel05.html

While there is plenty of evidence that a number of the founding fathers harbored significant religious skepticism, and one might reasonably argue that some, like Thomas Jefferson and John Adams, may have been partially motivated by enlightenment era rationalist skepticism and a desire to stifle religious dogma, but that wasn't the true explicit purpose of the Establishment Clause. Its primary purpose was to prevent the federal union from being jeopardized by religious disagreements.

While the colonies were dominated by protestants, the protestants were not monolithic. Anglicans, Calvinists, Methodists, Baptists, Congregationalists, Presbyterians, Unitarians, Quakers, etc. are all different from each other in theological beliefs and practices, and while many of the differences may seem trivial to an outsider or non-believer, they were not trivial to the true believers in the colonies.

The only way for the congregationalists in Massachusetts to feel safe from the influence of Anglicanism out of the Southern states under a federal government, is to make sure that the Federal Government has no power to establish or favor any one version of Christianity or to suppress another. The establishment clause allowed for the states to form a union without needing to resolve religious differences that would have been impossible to overcome.

As noted by /u/otolenghi, the establisment clause only restrained the Federal Government at the time. Until the 14th Amendment, and subsequent court cases, there was no general individual "freedom of religion", just a restraint on the federal government from weighing in. The 1st Amendment provided no protection against or freedom from the religion of your community, city, or state.