So we vaccinate 12 year old girls because they might have unprotected sex at some future date, but we don't vaccinate 12 year old boys because they haven't come out of the closet yet?

I realize that we're talking about 90% of a population vs. 10% (actual percentages are different I'm sure, but you get the point), but isn't there potential for this to give rise to a super-bug in the gay community, which then spills back over to the straight community and puts us back at square one?

Isn't the whole point to vaccines that we inoculate everyone so it just plain goes away?

To answer your last question, No the goal is not to eradicate HPV. It is too ubiquitous and has over 100 sub types. It is not like polio, where eradication is the goal. Reduction in the cancer deaths from the virus is the goal, and so the approach to the problem is different.

"but we don't vaccinate 12 year old boys because they haven't come out of the closet yet?"

You are talking about a 1% homosexual population. Though, really, the answer is probably that the vaccine works better in women in a certain age bracket. If it worked well on everyone, you can be sure that Merck would be including all men and women.