I sturggled long and hard with this one myself. I vaguely say I'm an atheist, but then the atheists around me assume I am one of them, and woo do they bug me sometimes! I have never found anyone with similar beliefs to mine. I deeply respect nature and people, but don't worship anything. If I were to go to church, it would be the UU church 10 miles away. Dh is agnostic. We go to churches for other peoples' weddings and for funerals. We firmly believe to respect the opinions of others.
I spent a lot of time researching cub scout packs in our area. I finally chose the largest close-by one--purposefully avoiding those associated with any particular church. Racially, ethnically, religiously diverse. The religious programs are there for people, most people do not participate. Ds LOVES it, and it has been great for him (he is very shy). Now that he's in, though, I've discovered what bothers me the most is the consumerism and obsession with media and things we don't find appropriate (like sleep-in laser tag--but maybe when he's a webelo I won't care?), and Boys Life is this crazy helter-skelter-can-you-read-it thing it wasn't when my brother got it. Dh disapproves of the rah rah Americanism, but his pack isn't so bad as some of the others we have seen/met.
Now, ds is sure he will be a boy scout. _IF_ he still wants to be one come 5th grade, I will hope for this troop--see their letter:
http://www.troop2bsa.org/position.html . It won't solve my religion issue (BSA does not recogize UU), but we will talk about that when he's 11 and feeling out for himself. If our pack changes in any significant way, we may switch to their related cub pack--though a 10 mil LA drive at 8pm is a bit much for my little guy on a school night

I say do some research in your area. I feel very, very fortunate to have options. We tried for 4H, but the only group here is homeschoolers only, and so self-righteous about it that I wouldn't join even I did homeschool! Campfire is 20-miles plus away and low income only.
We have also signed on to roots and shoots, but haven't officially joined or done anything--maybe this summer. Sounds promising.
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