Like the rest of society, the Boy Scouts have changed a great deal over the years. I got involved in scouting when my son wanted to join a couple of years ago. Religion has never been an issue. Yes, I am sure that there are still scoutmasters in the world who would make a stink about a kid if they found out he was an atheist, but I think you would have to work hard to actually find one. I tell my kid that being "reverent" means being respectful toward everyone's religious beliefs. If you can't manage that, in my opinion, you shouldn't be a boy scout or a scoutmaster.
As for sexuality, I'm pretty sure it's a "Don't ask. Don't tell." sort of policy. It's a relic of some bygone attitudes, I think. In the past, it wasn't unusual for kids to run around without clothes on at camps, and there was an idea of homosexuals getting worked into a frenzy in that situation. Now, there are usually enough mothers present in the campground that the kids will be keeping their clothes on all the time, anyway. More importantly, more people realize that it just isn't a really big problem. Gay people don't seem to react that way to the presence of naked members of the same sex. The regulations that are in place to protect kids against heterosexual pedophiles are more than enough to protect them from homosexual pedophiles as well. Most boy scout leadership is based on people who either currently have kids in scouts, or have had them in scouts in the past. In the past, that meant not many gay people participated. My guess is that as more gay people start traising children, and those children want to be boy scouts, those barriers will drop, but it will take some time.
Let's not throw the baby out with the bath, here. The Boy Scouts are an excellent, but not perfect, organization. In my experience, there is no barrier to participation based on either religion or sexual orientation, regardless of what the official rules say. (Granted, I haven't paid much attention to the sexual orientation difficulties, which I suspect are a bigger problem.) I suppose it's good to keep raising the issues, to keep pressure on that will eventually goad them into changes, but that takes time. In the meantime, there's no reason to keep your kid out of them based on those reasons, and there's no reason to try to force other kids out of the Scouts, either.