This is a really good question. I heard a scientist on NPR asked this question, and her response was that, "The HPV vaccine is a vaccine against a few types (out of more than 500) of this STD. However, in order to make it marketable, the manufacturer needs to tout it as a 'cancer vaccine,' not an STD vaccine." So, because men are not at risk for HPV-related cancer, they are not being vaccinated for it.
The same sort of thing happened with the Hepatitis B vaccine. It was marketed to teenagers and young men and women in the late 90s, and failed miserably. So the CDC recommended it be added to the mandatory vaccine schedule, and it's now given at birth, usually before a baby leaves the hospital.
The CDC knows that to get people vaccinated, they need be living under their parents' roof, and their parents need to be taking them to the doctor regularly. Teens don't visit the doctor as often, which is why this is being recommended for preteens.
Not saying it's a positive or a negative, just that that's the rationale.