Jotaro divorced his wife to protect her and Jolyne from the criminals he was fighting. The Joestar family has made a number of enemies over generations and Jotaro isn't necessarily the most-liked member. When we first meet him, he's giving his mom Holy all kinds of attitude even though she's trying to help get him out of jail.

Jotaro's even called Holy a b---h. If he can do that to his sweet mom, he's not going to be afraid to piss off some strangers and bad guys. So it's no surprise that there are people who might be looking for revenge against him and would use his family against him.

On top of that. Jotaro was always way fighting and basically didn't have time for his family. CBR says that over the years, Jolyne basically grew up fatherless. He could have just been honest with his family and told them that he kept his distance in order to protect them, but that conversation never happened and it seems like Jolyne became resentful. Getting a divorce was the ultimate separation that he felt would keep his family safe.

By the time Jotaro and his ex got a divorce, their relationship had already deteriorated. He was always away from home and didn't have a relationship with his daughter. But what little bond Jotaro and Joylne did have was basically destroyed after the divorce and the two didn't speak for years. In fact, Jolyne even changed the spelling of her last name from "Kujo" to "Cujoh."