By 1580 it does not seem that there was any good reason for the Protestant nervousness, even if some northern counties and northern and Border peers preferred Catholicism.
The king himself, a firm believer in his own theological learning and acuteness, was thoroughly Protestant.
But the preachers would scarcely allow him to remain a Protestant.

Their claims, as formulated by Andrew Melville, were inconsistent with the right of the State to be mistress in her own house.

In a General Assembly at Glasgow (1581) Presbyteries were established; Episcopacy was condemned; the Kirk claimed for herself a separate jurisdiction, uninvadable by the State.

Elizabeth, though for State reasons she usually backed the Presbyterians against James, also warned him of "a sect of dangerous consequence, which would have no king but a presbytery." The Kirk, with her sword of excommunication, and with the inspired violence of the political sermons and prayers, invaded the secular authority whenever and wherever she pleased, and supported the preachers in their claims to be tried first, when accused of treasonable libels, in their own ecclesiastical courts.

These were certain to acquit them.
James, if not pressed in this fashion, had no particular reason for desiring Episcopal government of the Kirk, but being so pressed he saw no refuge save in bishops.