All of the Tudor monarchs were plagued with plots and rebellions. The earlier insurrections that Henry VII had to deal with, were aimed at restoring the Yorkist line, and the later plots that Elizabeth contended with aimed to replace her with Mary Queen of Scots. In between, the rebellions were more about redressing grievances than overthrowing the Government.
In Scotland, James IV controlled his barons firmly, but the minority governments of James V and Mary were plagued with feuding for control of the Crown. By and large, the mass of the Scots people don’t seem to have been interested in rebellion – they just followed their Clan leaders. The overthrow of Mary was entirely a scheme for replacing her with a leader more palatable to the Lords, mainly for religious reasons. James VI worked hard to regain control over his nobles, and largely succeeded.