One of the areas that I've seen many scouts give back to a church is via a service project. Recently, one of the Scouts in our church's troop completed a service project where they put landscaping around our church's new sign.
I know of a number of churches in the area that have an outdoor shelter, or a renovated handicap ramp, or some other item that has been done as part of a service project by scouts. Many people think of service projects largely as an Eagle Project or a Gold Award Project. But why wait for then?
There's no reason that younger scouts can't participate in a food drive to help a church's food pantry, or go visit church shut-ins, or even plant flowers at the church at a den meeting. Look at the activities your scouts are encouraged to do for advancement, and I bet there's something that can be done to benefit the church your scouts meet at. Doing so will let the scouts see the benefits of their service work each week when they show up for their weekly meetings, and also help foster better relations between the church and the scout unit.