Answer from Danavir Goswami
Yes, hatred comes from God, “I am seated in everyone’s heart, and from Me come remembrance, knowledge and forgetfulness.” The living entity’s hatred is based on forgetting the truth about the Lord and oneself. In that condition he hates and envies the Lord (dvesah). Srila Prabhupada writes:
When one becomes envious of Krsna, or the Supreme Personality of Godhead, one thinks, “Why should Krsna be the all and all? I’m as good as Krsna.” These two items, desire to be the Lord and envy of the Lord, are the beginning cause of material bondage.
(Srimad Bhagavatam 3.27.20 Purport)
The Lord mercifully allows the living entities to exhibit their free will even when it is misdirected.