Drogon for Khal Drogo, her first husband and sun-and-stars; Rhaegal for Rhaegar, the brother she never met but everybody spoke highly of as “The Last Dragon” despite his reputation for kidnapping and raping Lyanna Stark; Viserion for Viserys, who got himself killed in Season 1 but was still key to Dany’s journey and probably would have been her husband if he hadn’t wanted Drogo’s army.
Daenerys named her dragons for three of the men who were most important to her, even if they weren’t all her favorite people.