Being an Eagle Scout myself, I will vouch for the BSA. They are an organization that does their part to influence the lives of young males in a constructive manner and to teach them moral and ethical values that they will take with them to the rest of their lives. Holding true to their moral convictions and shielding them from the influence of homosexuality is part of that. They are a private organization heavily influenced by the teachings of Christianity, and they have the right to act however they please. You may not like it, you may think it's hatred and bigotry, but the fact of the matter is they have been at this for WAY longer than you have, and I think the results speak for themselves.
As Inflexus above has pointed out, there' an actual reason behind this prohibition. It's for the protection of the Scouts themselves against sexual predators. When we go out on our campings we are out there for several days or even weeks, away from the protection society at large provides, with the organization & its leaders being pretty much the only source of protection we have. If there is one among their ranks who secretly has sexual wantings for the young males, who else is going to stop him? They're out in the middle of the woods, far away from the rest of civilization, and they are at greater risk there. This is a safety measure put in place to prevent that scenario from happening, and it swings both ways; adult heterosexual males wanting a position in the leadership must pass training in protection as well as personal screening. I will admit upon reflection that it is a bit of a generalization, but the reasons are well-intentioned.