For all the good that the sixteenth-century Protestant movements may have brought to the Western Church in the way of doctrinal reforms, there was at least one outcome that wrought inestimable damage—namely, schism. It is not that there were no schisms before the sixteenth century. Neither is it the case that the early Protestants desired schism; in fact, they made a fairly strong case that it was the Roman Church’s doctrinal innovations and resistance to reform that caused and perpetuated the schism. It is also true, however, that Protestants, almost as soon as there were Protestants, exhibited a persistent inability to get along with one another.
From the 1520s on, Protestant history includes stories of disagreements over baptism, the Lord’s Supper, liturgy, free will and predestination, the relationship of the church with civil government, and biblical interpretation, which in many cases was the source of the disagreements. It did not take long for Protestants, as well as Roman Catholics, to draw up new confessions of faith that distinguished their own particular groups. Despite the occasional, lone voices calling for unity, by the end of the sixteenth century, instead of one unified church in the West, there were now Roman Catholic, Lutheran, Reformed, and a number of Anabaptist and “radical” churches, each with its own confessional standard. Thus began denominations in the West. These initial breaks were only the beginning, though, as the disputes and divisions continued. Once Pandora’s box was opened, once the precedent was set that any doctrinal disagreement could justify starting a new church, the horrific possibility of schism that was realized in the sixteenth century evolved into the accepted habit of schism in the seventeenth and eighteenth. Debates ensued now over the interpretation of the new confessional standards—including what subscription meant and whether it was even necessary—all of which led to further contentions and divisions.
This habit of schism, transferred from the Old World, became compulsive in the New World. In American soil, nourished by autonomous freedom from old traditions and by optimistic visions of finally making the church what it was supposed to be, the seeds of schism proliferated, grew, and flourished.
Implicated in this guilt were, among many others, the Presbyterians, whose Westminster Confession of Faith and Catechism served as confessional standards. Throughout the eighteenth century, a significant number of Presbyterians had various reservations about signing on to these standards, and many simply refused to subscribe at all. Aside from the doctrinal teaching of the Westminster standards, in the wake of the evangelical revivals in England and especially the Second Great Awakening in North America, Presbyterians further divided over their openness to the revivals (so-called “Old Lights” versus “New Lights”).
Source: Keith D. Stanglin - "The Restoration Movement, the Habit of Schism, and a Proposal for Unity", by Dr. Keith D. Stanglin, in Christian Studies, Volume 28, August 2016, http://austingrad.edu/Christian%20Studies/CS%2028/Proposal%20for%20Unity.pdf