Cizik disclosed that he had voted for Barack Obama in the primaries, that younger evangelicals "know gay people" and aren't as "threatened" as their parents. He also suggested that Sarah Palin's positions on global warming – which he defines as "creation care" – were like burning the Bible.
NAE's Anderson explained to the members of his board of directors that Cizik did not "appropriately represent the values and convictions" of the 45,000-church strong organization.
"Although he has subsequently expressed regret, apologized and affirmed our values there is a loss of trust in his credibility as a spokesperson among leaders and constituents," Anderson said in a Dec. 5 letter posted on NAE's Web site. "Our NAE stand on marriage, abortion and other biblical values is long, clear and unchanged."
NAE President Leith Anderson and Cizik both declined interviews with ABCNews.com.
"The classical church feels a bit threatened by the emerging group who say, 'I think God cares about gay people: I have a gay sister or brother. I have faith in Christ and I feel great compassion for my family members,'" said Adam Hamilton, pastor of the United Methodist Church of the Resurrection in Leawood, Kan., the largest such congregation in the country.
"There are yesterday and tomorrow evangelicals and Rich captured the sentiment of many of tomorrow's evangelicals," he said of Cizik's resignation. "Rich may not be the cause of it, but NAE is going to look at lot more like Richard's view or it will be 10 percent of the size it is today."
Until now, Cizik had survived attacks from James Dobson's Focus on the Family, which previously called for Cizik's resignation after he declared global warming a top priority.
Tom Minnery, senior vice president of Focus on the Family, concedes a growing awareness among evangelicals that so-called "creation care" is important, especially among the young.
"But Rich seemed to be saying that this issue was number one, and if you believe that abortion is the taking of innocent life and anything else is more important then he had developed a narrow agenda," he told ABCNews.com.
Pro-life still "resonates so deeply" with evangelicals, said Minnery. "It's still a vital movement this long after Roe v. Wade."
Minnery said that issue and the ban of gay marriage in three states show that Christians are resolute. But he acknowledges attitudes toward gays are "shifting" among younger evangelicals.
But a pre- and post-election poll conducted by the nonprofit Faith in Public Life showed religious voters placed a greater priority on the economy, healthcare and Iraq over same-sex marriage and abortion.
In this survey of 1,277 voters, 86 percent of white evangelicals said their elected leaders should find ways to reduce abortion, expanding adoption and increasing economic support for women who want to carry their pregnancies to term.
Only one in five evangelicals said an agenda focused primarily on abortion and same-sex marriage best reflects their values.
"The Christian right has hijacked the term 'family values' and used it as an anti-gay weapon," said Jacki Waring, a 25-year-old evangelical who lives in Washington, D.C. "I find this repugnant."