I would agree with auntlori in that there was religious freedom in a general sense. However in most colonies there was one church in which everyone belonged. Not really a choice of religion.
I agree. In terms of religious freedom generally, there was plenty. In other words, one could establish whatever church or religious institution one wished--though most were, of course, Christian. There was plenty of opportunity to establish a faith-based community; however, once one committed to that community, there was not much freedom. Because the church often served as the only religious, social, and judicial (legal) system in the town, it was incumbent upon every citizen in the community to obey the edicts of the church (i.e., how to live, when to attend church, how much money should be given to the church). If anyone was unable or unwilling to live in such a theocracy, the alternative was usually to leave. Eventually, when enough people were unwilling to live under this type of government, things changed and the move toward Revolution and complete emancipation began.
In order to write an essay about this, you will want to look at both sides -- you'll want to cite ways in which there was and was not religious freedom. Then you'll want to make some conclusion about the sort of net balance or net amount of freedom.
On the one hand, there was a lot of religious freedom. In most colonies, all religions (mainly Christian sects and Judaism) were tolerated. You could belong to whatever sect you liked and you were free to worship.
On the other hand, all colonies had established churches. (They got to choose their own, which is religious freedom of a sort.) You had to pay taxes to support that church whether you belonged to it or not.
If I were writing an essay, I would use these as my starting point and provide details about each of these basic ideas.