That's understandable, but it's like with any sort of contact with fallible entities. The fact that, for example, the fact that the Jews killed Jesus doesn't mean that we should not treat them any differently; for bear this in mind, the ultimate responsibility for the death of Christ is not the government, Romans, and the Jews, but God Himself:
20 But as for you, ye thought evil against me; but God meant it unto good, to bring to pass, as it is this day, to save much people alive.
- Genesis 50:20
14 But ye denied the Holy One and the Just, and desired a murderer to be granted unto you;
15 And killed the Prince of life, whom God hath raised from the dead; whereof we are witnesses.
16 And his name through faith in his name hath made this man strong, whom ye see and know: yea, the faith which is by him hath given him this perfect soundness in the presence of you all.
17 And now, brethren, I wot that through ignorance ye did it, as did also your rulers.
18 But those things, which God before had shewed by the mouth of all his prophets, that Christ should suffer, he hath so fulfilled.
- Acts 3:14-18
Now, if you're an American, and wondering when to rebel and overthrow government when the power above us becomes tyrannical... that I cannot give any advice. However, Jesus did say that we should be "Wise as serpents and harmless as doves" (Matthew 10:16). Also, "Render therefore unto Caesar the things which are Caesar's; and unto God the things that are God's" (Matthew 22:21). Furthermore, Paul said what he has said (Romans 13:1-4) in the time when persecution can arise at any moment (of course, that doesn't mean we must obey against our conscience).
We can, however, defend ourselves as when Jesus said to His disciples to sell their cloak and buy swords, He didn't say that to later prove a Pacifist's point. He said what he had said because of what was to come: arrest and persecution. They are to flee and defend themselves, if necessary, but not ... to wage a holy war which is why Jesus said "...all they that take the sword shall perish with the sword" (Matthew 26:52).
