The following is from Douglas Moo’s NIV Application Commentary on Romans.
Where is the exception?
As we noted above, the key question most of us ask when we come to Romans 13 is not “What does it mean?” but “Where is the exception?” Since it is taught so consistently in Scripture, we do not have much difficulty coming to grips with the idea that God has ordained all governing authorities and that we must recognize that we stand under them. But we do have difficulty with the apparent demand of Romans 13 that we always do whatever any governmental authority tells us to do. We know there are exceptions in Scripture itself, and we believe deeply that it was contrary to God’s will for Germans to obey their rulers and help the Nazis kill millions of Jews, Poles, Russians, and so on. But how can we justify any exceptions in Romans 13? On what basis can we allow exceptions without doing violence to these verses? Seven possibilities deserve to be mentioned – listed here in order of least probable to most probable.
(6) In our interpretation of verses 3-4, we suggested Paul admits only of the possibility that states will reward good and punish evil because he is implicitly thinking of the ideal state – the state when it operates as God intends it to. Paul may, therefore, be calling on Christians to submit to governing authorities only as long as they are fulfilling their mission, under God, to restrain evil and encourage good. When a state ceases to do so, Christian are free to disobey its mandates.
The problem with this view is that Paul does not explicitly qualify his command with any such restriction. Yet this idea has merit, for it is difficult otherwise to explain why Paul ignores the possibility that the state may punish good and reward evil. He is describing how the state is supposed to function under God and is calling believers to submit to states that function in that way. Perhaps there is room in what he says to allow believers to turn against the state when it turns against God – as it does, for example, in Revelation.
[Compare with Hodge “It was his object to lay down the simple principle, that magistrates are to be obeyed. The extent of this obedience is to be determined from the nature of the case. They are to be obeyed as magistrates, in the exercise of their lawful authority. When Paul commands wives to obey their husbands, they are required to obey them as husbands, not as masters, nor as kings; children are to obey their parents as parents, not as sovereigns; and so in every other case.”]
(7) In demanding “submission” to the state, Paul is not necessarily demanding obedience to every mandate of the state. Key to this restriction is the recognition that the word “submit” (hypotasso) in Paul is not a simple equivalent to “obey” (hypakouo). To be sure, they overlap, and in some contexts, perhaps, they cannot be distinguished (cf. 1 Peter 3:1, 6). Moreover, submission is usually expressed through obedience.
Nevertheless, submission is broader and more basic than obedience. To submit is to recognize one’s subordinate place in a hierarchy established by God. It is acknowledged that certain institutions or people have been placed over us and have the right to our respect and deference. In addition to rulers (see also Titus 3:1), Paul also calls on believers to submit to their spiritual leaders (1 Cor. 16:16) and even to one another (Eph. 5:21; i.e., in the ways Paul outlines in 5:22-6:9). Christian slaves are to submit to their masters (Titus 2:9), Christian prophets to other prophets (1 Cor. 14:32), and Christian wives to their husbands (1 Cor. 14:45 [?]; Eph. 5:24; Col. 3:18; Titus 2:5). In each case, one person is to recognize the rightful leadership role that another human being has in his or her life.
But implicit always in the idea of submission is the need to recognize that God is at the pinnacle of any hierarchy. While not always explicit, Paul assumes that one’s ultimate submission must be to God and that no human being can ever stand as the ultimate authority for a believer.
The parallel between a Christian’s submitting to government and a wife’s submitting to her husband is particularly helpful. The wife is to recognize that God has ordained her husband to be her “head,” that is, her leader and guide. Thus, she must follow his leadership. But Paul would never think that a wife must always do whatever her husband demanded.
I once counseled a Christian woman who took her need to submit to her husband so seriously that she felt obliged to obey him by engaging in sex with him and another woman at the same time. I urged her to recognize that her ultimate allegiance was to God, the authority standing over her husband. She needed to follow the higher authority in this case and disobey her husband. But this did not mean that she was simply to dismiss her husband or to renounce his general authority over her.
In a similar way, it seems to me, we can also, as believers, continue to submit to governing authorities even as, in certain specific instances, we find that we cannot obey them.
[In other words, Paul tells us not to overthrow the rulers, but to be subject to them. He does not tell us they have divine authority that must be obeyed in whatever they command.]