Another thing to keep in mind was that the initial trials were only using cervical cancer endpoints - the association between HOV infection and cervical cancer is really strong. At that time, vaccinating boys provided only indirect protection (you couldn't infect a female partner), rather than direct protection (you won't be infected) in the context of cervical cancer.
Women prior to sexual debut were the biggest "bang for the buck" and the obvious first recommendation target.
Researchers both at universities and in private industry then started working on other populations based on alternative endpoints.