This article only mentions sexual orientation:
http://www.sfgate.com/news/article/Boy-Scouts-could-lose-tax-break-for-gay-ban-4292197.php
The bill itself includes religion and religious affiliation, so it would still be in effect if the BSA allows gays but still excludes atheists:
http://www.leginfo.ca.gov/pub/13-14/bill/sen/sb_0301-0350/sb_323_bill_20130219_introduced.html


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