After graduating from UNCSA and before attending the Yale School of Drama, Jonathan had a daughter, who is currently seven years old. During his June 2020 interview with People, Jonathan said that his priority is giving his daughter a proper education on Black history. "She has to understand that it's actually not 'Black history' — it's American history," he said. "The way it's taught now, it's honestly the Jim Crow system of separate but equal. We'll give it one month, 12 pages in the history book . . . we'll talk about Harriet Tubman, Rosa Park, MLK, then we'll give you a little quiz about it. And that's it."
For Jonathan, it's also important for his daughter to celebrate her Blackness. During a June 2020 interview with W, the actor recalled a conversation he had with his daughter, who was frustrated "because her hair won't fall down — her hair goes up." In response, he told her, "You have a crown. That's why your hair goes up. Your hair, your crown, came from daddy, came from his mama, came from his father, came from his sister. Sometimes that crown can get you in trouble in this world, and it's not right. And some people want to take that crown from you."