From our perspective as Americans today, there was not as much religious freedom in the colonies as there should have been.

There was some religious freedom.  For the most part, people were free to practice any sort of Christian religion.  There was very little in the way of persecution of any Christian church.  

Even so, we would not say that people in those times enjoyed true religious freedom.  For one thing, there were colonies where people were persecuted for their faith.  This particularly happened in Massachusetts, where there are even instances of people being executed for being Quaker missionaries.  For a second thing, most of the colonies had established, official churches.  People had to pay taxes to support these churches, regardless of whether they believed in them.  We would not think either of these things is in any way acceptable today.