During Milton's time, it seemed that having people stand up to government and church officials was becoming a bit more popular. The aristocracy in the Church didn't like this, especially since if someone was complaining against the church, they were complaining against the government, since the two were inseparable. However, people were getting braver and there was more political turmoil going on during this time period as well. Milton was definitely one of these people in that he's regarded a radical and he went to great lengths to criticize the aristocracy in the Church. The thing I was impressed with Milton was his use of imagery to portray the Church's crimes in such a vivid and blatant manner. It shows how this was during such a time of turmoil and unrest. As it was, Milton was almost hung several times for his radical writings.
Milton was showing other people that one should criticize the Church for its wrongdoings, calling it a duty. He says in "Against Prelaty" that "hence appear the right I have to meddle in these matters, as before the necessity and constraint appeared." He's basically telling others that it's alright to criticize the Church/government, something they were trying to discourage. This shows how the political structure was weakening.
Milton was blatant in his criticism, showing that he wasn't afraid of how the church and government would react to his accusations. He says some pretty intense things. For example, in "A Reformation," he compares the soul under the influences of the church to a type of bird whose "pinions now broken and flagging, shifted off from herself the labor of high soaring anymore, forgot her heavenly flight, and left the dull and droiling carcass to plod in the old road and drudging trade of outward conformity." That's some pretty heavy handed stuff. It shows Milton's willingness to hit the Church hard, and not be scared of backlash, though there definitely was backlash. It just shows the political strife that's going on during this time. It also shows Milton's courage, or perhaps insanity in his writings, which is interesting. I'm curious to see what kind of political references he may be making in Paradise Lost. I'll have to look for that more.