My son is a boy scout, and he did all the years of cub scout as well (tiger, wolf, bear, Webelos I and II).
I do not agree with their stance on homosexuality - and when it became obvious that the organization's administration was very anti-gay, I was ready to pull him out - *but* when I told my (gay) mother this, she asked that I not take him out.
Her reasoning? Yes, the administration is anti-gay, but the people who actually run the individual troops/packs are not necessarily in agreement with the adminstration's stance. The idea of who a boy scout should try to be is a very good thing for today's kids - someone who is honest, loyal, helpful and hardworking. BSA provides opportunities for kids to get out and do things they normally don't necessarily do - camping, Klondike Derby, swimming, CPR/First Aid, etc - and to do community service with no expectation of payment. It also provides boys who have little or no male role models in their lives quite a bit of male interaction. It also reinforces spending time with family and being interested and involved with your world. And, last, but not least, having your Eagle Scout Badge is quite an honor - and means something when applying for jobs as an adult, applying for scholarships, etc.
So, really, you have to weigh the pros and cons - and get to know the leaders in your community, then make the decision.
I have had no problems with the leaders in my son's pack enspousing the administration's beliefs.