“That was the government he instructed them to obey.”
Would you obey Caesar if he ordered you to kill an innocent Christian?
Christians also made it very clear, in the days shortly after Christ died, that “We must obey God as ruler rather than men.”
When earthly rulers command us to do something contrary to God’s law, we should simply refuse to obey.
The situation is also complicated for us, relative to those faced by 1st-century Christians, by the fact that we are Caesar, to some extent. As American citizens, collectively we are Caesar. Thus we function to some extent both as ruler and subject. Also, our government is based on the Constitution. Any official breaking that compact is arguably not legitimate.
But it is simply untrue that we can decide to disobey orders from a ruler that do not conflict with God’s laws simply because we think the government is unrighteous. It would have to work pretty hard to be more unrighteous than the one Paul spoke of as being necessary to obey.