Why is the ACLU "attacking" the Boy Scouts? Simply put, because they believe the American government (at every level) ought to cease subsidizing the BSA's longstanding pratice of religious and sexual discrimination against minority groups such as homosexuals and infidels. As ACLU Executive Director Linda Hills put it, "The Boy Scouts can't have it both ways. If they truly are a private religious organization, free to engage in any form of discrimination they choose, then they are not entitled to a government subsidy. Tax dollars should not be spent to promote intolerance."
Perhaps conservatives such as Steve Boggess would like to make the case for having substantial federal, state, and municipal subsidies to private religious groups, but it will be difficult to square such an argument either with existing federal, state, and municipal antidiscrimination laws or with the traditional conservative vision of minimal government in general and highly circumscribed government interference in the marketplace in particular.
Far from being "adamant in their goal of erasing God from not only this privately funded organization" the ACLU is trying to ensure that truly religious organizations remain truly private and hence free from both government subsidy and interference. The BSA is quasi-private and quasi-religious, yet they expect the American government to continue publicly funding their activities despite their flagrant disregard of uncounted civil rights laws. You can have the cake or you can eat it, folks. Take your pick.