God made everything for God. That's hard to comprehend when considering dictators and mass murderers like Pol Pot, Stalin and Hitler.
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After repeated but unhedded warnings by Jeremiah to Israel for their sin, God used king Nebuchadnezzar of Babylon as an instrument of judgment against Israel. In Jeremiah 25:9 Nebuchadnezzar is referred to as "my servant". (See entire chapter) After the 70 years captivity was accomplished The Lord used Cyrus of Persia to punish the Babylonians for their mistreatment of captive Israel, to liberate them and for the purpose of rebuilding Jerusalem. "That saith of Cyrus, He is my shepherd, and shall perform all my pleasure: even saying to Jerusalem, Thou shalt be built; and to the temple, Thy foundation shall be laid." (Isaiah 44:28) "Thus saith the LORD to his anointed, to Cyrus, whose right hand I have holden, to subdue nations before him; and I will loose the loins of kings, to open before him the two leaved gates; and the gates shall not be shut;" (Isaiah 45:1) In summary: "The king's heart is in the hand of the LORD, as the rivers of water: he turneth it whithersoever he will." (Proverbs 21:1)
Consider this from Daniel 4:17: 17 This matter is by the decree of the watchers, and the demand by the word of the holy ones: to the intent that the living may know that the most High ruleth in the kingdom of men, and giveth it to whomsoever he will, and setteth up over it the basest of men. We must understand that God rules this world’s governments; even if the most evil people are seemingly in charge.
If the question is referring to the mention in the cited verse of thrones, dominions, principalities, and authorities, my understanding is that these entities are not related to earthly governments, but are orders or ranks of spiritual beings, similar to the mention of principalities made by Paul in Romans 8:38. Evil on earth (whether individual or governmental) is entirely the working of the devil through sinful human agents. Christians are admonished in passages such as Romans 13:1-7 and 1 Peter 2:13-17 to obey earthly governments. They can seek to avoid or escape earthly persecution or punishment, but they have a higher duty of allegiance and obedience to God in the case of irreconcilable conflict, which may call upon them to resist or combat established authority. However, they must also be prepared (if necessary) to bear the temporal consequences of their actions (no matter how unjust those consequences may be), as Paul and Peter both did when they were arrested and ultimately martyred for their faith. Those who unrepentantly perpetrate such injustices will be accountable eternally (if not also temporally) for their actions.
What this question is really asking is, "If God is in control why does he allow evil to exist"? The answer is that sovereignty will not usurp free will until judgement day. God created angelic beings with free will because he desired their love and worship freely given. But Satan wanted to be worshipped instead of God, so he led a rebellion that enticed 1/3 of the angels to freely join him. God created human beings with free will because he desired their love and worship, freely given. He even gave humans free reign over the entire planet earth, with only 1 prohibition. But they too were enticed by Satan, wanting to be like God, knowing good and evil. They sinned and their rebellion brought sin and evil into God's created earth. Every human being inherits this sinful nature. Our predisposition is rebellion against God - evil and wickedness - all the time (Psalm 14:3). Look what Paul says in Colossians 1:19 "Once you were alienated from God and were enemies in your minds because of your evil behaviour." And again in Colossians 1:13 "For he has rescued us from the dominion of darkness and brought us into the kingdom of the Son he loves, in whom we have redemption, the forgiveness of sins." God's will is expressed in Colossians 1:19-22. Through Jesus sacrifice on the cross, God is reconciling all things to himself, including things in heaven and on earth, by making peace through Jesus shed blood on the cross. This offer of reconciliation is open to every human being. Every human being has the free will to believe in Jesus and accept him as their saviour, or reject him and face God's judgement. All evil that exists on the earth today, or at any time in the past or future, is simply the result of people rejecting God's grace and free gift of eternal life, and choosing instead to continue indulging their sinful nature. The result of all sin is evil, wickedness and death. But the ultimate justice will come on judgement day. All acts of evil, not atoned for by the shed blood of Jesus, will face eternal punishment in hell. God's sovereignty is most clearly demonstrated in the lives of his chosen saints (believers in Jesus). Look at how God protected Paul and enabled him to preach the gospel of Jesus Christ throughout the known world. Look at the growth of the Christian church in our age, now encompassing nearly 2 billion people. When Jesus came as a human being, part of his mission was to reclaim the earth for the kingdom of God. Jesus announced the coming of the kingdom. Every person who came to faith in Jesus expanded the kingdom of God on earth. Every person who is born again by the Holy Spirit, and lives a new godly life, is pushing back the presence and power of evil in our world. If every human being accepted God's offer of reconciliation, the power of evil would be dramatically reduced in our world today. God will show us what a world looks like where he is in control when he establishes the millennial rule of Jesus on earth. Then Jesus will show us what life is supposed to look like without the presence of sin and evil, when he recreates the heavens and earth. God is not being slow in judging evil, he is being patient, waiting for us to repent as he doesn't want anyone to perish (2 Peter 3:9). God's offer of reconciliation was even open to Hitler, Stalin and Pol Pot (and ISIS too), but they exercised their free will and rejected it. Now they face his judgement. God is exercising his sovereignty to extend us his grace now and his judgement will come at the appointed time.
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