For God to hate someone seems, to us, contrary to His very character. Scripture tells us "He who does not love does not know God, for God is love." (1 John 4:8). Thus, as a culture, we have this idea that God just loves everyone, and cannot hate anyone. Hate the sin, love the sinner, as the cliche goes. And it is 100% true.
This makes it incredibly confusing when we come across verses like Romans 9:13, a personal favorite proof texts for many errant teachings within the Church. If God is really love, how can He say "...Jacob I have loved, but Esau I have hated"?
The first key to understanding this verse is to take note of the other part: "As it is written...". A key hermeneutical principle is that Scripture interprets Scripture. Reading a single Bible verse alone is guaranteed to cause confusion, and even lead you astray. Thus, we must take every relevant Scripture into account. This often requires reading not only the current chapter, but often even reading entirely different sections. The phrase "it is written" tells us that this Scripture requires us to know at least one other Scripture in order to understand it. In this case, the beginning of the book of Malachi.
But for a moment, I want us to shelve that thought, and head instead to the book of Luke. In Luke 14:26-33, Jesus tells us "“If anyone comes to Me and does not hate his father and mother, wife and children, brothers and sisters, yes, and his own life also, he cannot be My disciple. And whoever does not bear his cross and come after Me cannot be My disciple. For which of you, intending to build a tower, does not sit down first and count the cost, whether he has enough to finish it— lest, after he has laid the foundation, and is not able to finish, all who see it begin to mock him, saying, ‘This man began to build and was not able to finish’? Or what king, going to make war against another king, does not sit down first and consider whether he is able with ten thousand to meet him who comes against him with twenty thousand? Or else, while the other is still a great way off, he sends a delegation and asks conditions of peace. So likewise, whoever of you does not forsake all that he has cannot be My disciple."
These are some very harsh, very strong words. Here, the same Jesus who tells us to love our neighbors, and even our enemies, tells us that we must hate our own families. This would seem to be a grand contradiction. That is until we understand hatred in terms of degree.
When love is alone, it is a fairly simple concept. But what about when it has competitors? What if one thing you love conflicts with another thing you love? You now have a choice to make. Your parents, your spouse, your children, your brethren, even your life, are all very important. Here, however, Jesus says if you want to be His disciple, you must choose Him every time. If your parents say "give up this Jesus thing, or we're disowning you", forfeit your relationship with them. If your spouse says "it's Christ or me", be ready to sign those divorce papers. You get the idea.
With that in mind, let's follow Paul back to Malachi, where we find the original "Jacob I have loved, Esau I have hated". A closer look at the context of both Romans 9:13 and Malachi 1:1-3 reveals that actually, God didn't literally hate Esau. Rather, Esau is used as a representative of the nation that would be descended from him (Edom), which would not receive the same blessings as the nation that would be descended from Jacob (Israel).
In the Amplified Version, Malachi 1:2-3 reads like this: “I have loved you, says the Lord. Yet you say, How and in what way have You loved us? Was not Esau Jacob's brother? says the Lord; yet I loved Jacob (Israel), But [in comparison with the degree of love I have for Jacob] I have hated Esau [Edom] and have laid waste his mountains, and his heritage I have given to the jackals of the wilderness. [Rom. 9:13, 16.]”
Reading further on confirms this interpretation. Verses 4 and 5 (back to the NKJV) say "Even though Edom has said, “We have been impoverished, But we will return and build the desolate places,” Thus says the LORD of hosts: “They may build, but I will throw down; They shall be called the Territory of Wickedness, And the people against whom the LORD will have indignation forever. Your eyes shall see, And you shall say, ‘The LORD is magnified beyond the border of Israel.’"
Rather than referring to the brothers themselves, therefore, God’s statement that He hates Esau actually refers to His plan for the nation of Edom, who were descended from Esau. While Israel, born of Jacob, remains to this day, the nation of Edom does not. But Esau’s own eternal fate is not mentioned in the Bible. While it’s possible that he stands condemned, he could also have repented of his sins, and we could meet him in Heaven. Based on Jacob's own reunion with him in Genesis 33, this seems likely. Rather than being antagonistic to Jacob, as Edom was to Israel, the reunion is quite emotional, with Jacob even saying to his brother "...inasmuch as I have seen your face as though I had seen the face of God, and you were pleased with me." (Genesis 33:10).
Thus, it is beyond clear that God's hatred of Esau refers to the degree of preference He showed to Edom in relation to Israel, not to His everlasting emotional disdain for the man. We therefore have no need to be disturbed by the idea that God might hate someone, nor do we need to follow suit and hate certain people. Instead, we must obey God's direct commands to love even our enemies in order to be like our Father in Heaven (Matthew 5:43-48), and to live at peace with all men, so far as it depends on us (Romans 12:18).