There was also several congregationalists , who favoured autonomy for individual local churches . Their most influential divines was Thomas Goodwin , Philip Nye , Sidrach Simpson , Jeremiah Burroughs , and William Bridge . They was often called the " dissenting brethren " in the Assembly . They have sometimes been labelled " Independents " , but they rejected this term . The Assembly members for the most part reserved the label " Independent " for separatists who left the established church . The congregationalist divines cannot be equated with separatists and Brownists , as they had accepted episcopal ordination and remained in the Church of England . Their influence was assisted by the success of Oliver Cromwell and his New Model Army in the ongoing civil war . Cromwell and many others in the army supported congregationalism .