The Washington-based Family Research Council “advances faith, family and freedom in government and culture from a Christian worldview,” according to its profile on the website of GuideStar, the nation’s premier philanthropic rating agency. GuideStar gives the FRC a “silver” rating for demonstrating a “commitment to transparency.” But the top of the profile page also declares: “This organization was flagged as a hate group by the Southern Poverty Law Center.”

GuideStar announced this month that it would classify 46 nonprofits...