I have been taking a series of courses on reformation-era Europe. Having just completed a general course on the Reformation, I am now completing a course on the Tudors and Stuarts in England, a period of time whose history is highly colored by the Reformation.
One of the issues that Protestants had with the Catholic Church (and later with the Anglican Church) was the church hierarchy. Of course, the Pope always came in for criticism (this probably being too mild a word for burning in effigy) by English protestants, but bishops and other elements of church hierarchy also came in for attack. In fact, the Presbyterians, probably the largest non-Anglican Protestant sect in 17th century England, took their name from the presbyters, who were essentially a council of laymen or elders who ran the church (as an alternative to Popes and bishops and such).
One of the difficult issues for the modern American mind to wrap around is the state involvement with religion on these times. Taking just this one issue of church organization and hierarchy, we see a dizzying back and forth in the Anglican Church as a result of swings in religious affiliation and outlook of the monarch and the Parliament. Bishops get tossed from the Anglican Church, then Bishops are reinstated, then they get tossed, and then they get reinstated. All this punctuated by the occasional execution or locking in the Tower of the odd bishop. It was deadly serious at the time, but seems a silly pursuit for government today.
Except, I guess, in Connecticut, where the spirit of Oliver Cromwell and the Roundheads is alive and well. Because, apparently, the state legislature has introduced a bill to remove priests and bishops from the management of Catholic Church corporations and insist on a council of laymen instead. Weird how history repeats itself, even when you thought it was most unlikely to do so.
Disclosure: I am not Catholic, nor Presbyterian, nor particularly religious.