Romans 13:1 says, "Let every person be in subjection to the governing authorities. For there is no authority except from God, and those which exist are established by God." If this is so, what about the bad governments like the Nazis or the communist regimes where they killed millions? If God is the one who sets up governments, are we supposed to obey those bad governments?
The answer is no.
We are to obey governments unless they violate Scripture. Acts 5:29 says, "We must obey God rather than men." Whenever a government violates Biblical teaching, Christians are obligated to disobey that government. For example, if a government were to declare that we should kill all Asians or immigrants or people with Down's syndrome, we should disobey. Governments are run by people and often become corrupt. Furthermore, the Bible never tells us to obey governments in contradiction to the revealed Word of God.
In the Old Testament, God sent the Israelites to destroy different nations. Technically speaking, we could say that God set up those various governmental systems that He told the Israelites to destroy. But when systems become ungodly and anti-Christian, they are no longer properly representing God and should not be obeyed.
Are we seeing a conflict or a contradiction? Not at all. Let's take, for example, Exodus 20, where we see two commandments: obey your parents and do not murder. We can see that our parents are the authorities above us even as governments are and we should obey them. But, what should we do if our parents tell us to murder someone? Should we obey? Of course not. Obedience to our parents is only proper when it's consistent with the rest of the Scriptures. Likewise, submission to the governmental systems is only proper when it is consistent with Scripture.
Finally, let's look at Rom. 13:6-7, "For because of this you also pay taxes, for rulers are servants of God, devoting themselves to this very thing. 7 Render to all what is due them: tax to whom tax is due; custom to whom custom; fear to whom fear; honor to whom honor." Notice that Paul says that the rulers are servants of God. This is the context of the submission that is mentioned at the beginning of the chapter. If these rulers are no longer servants of God and if they contradict Scripture, they are not to be obeyed.