My Scout troop met in a church, but that was about the extent of it; we never discussed religion. However, this was in a northern state (Ohio). I've seen that many scout troops in the Deep South are a lot more religious and homophobic.
In my view, Scouting is definitely worth supporting, but since there is so much variation between individual troop organizations, that one should eschew giving money to the National organization and instead find a local troop whose values you believe in and support them.