By Dan Gilgoff, CNN.com Religion Editor

A New York Times column by outgoing Executive Editor Bill Keller has unleashed a hailstorm of online criticism among religious bloggers and conservative activists. The fact that the column compares religious believers to folks who think that space aliens are residing on Earth is just the beginning.

Keller’s column, “Asking Candidates Tougher Questions About Faith,” argues that the crop of candidates competing for the White House next year should be grilled on their religious beliefs and on how those beliefs inform their political views.

That’s especially true, Keller reasons, because many of this year’s GOP contenders hail from “churches that are mysterious or suspect to many Americans.”

Here’s Keller:

Mitt Romney and Jon Huntsman are Mormons, a faith that many conservative Christians have been taught is a “cult” and that many others think is just weird. … Rick Perry and Michele Bachmann are both affiliated with fervid subsets of evangelical Christianity — and Rick Santorum comes out of the most conservative wing of Catholicism — which has raised concerns about their respect for the separation of church and state, not to mention the separation of fact and fiction.

One of the Timesman’s key concerns is that these candidates will put their religious faith first - above the national interest and the laws of the land:

I do want to know if a candidate places fealty to the Bible, the Book of Mormon (the text, not the Broadway musical) or some other authority higher than the Constitution and laws of this country. … I care a lot if a candidate is going to be a Trojan horse for a sect that believes it has divine instructions on how we should be governed.

To that end, Keller announces that he has sent customized questionnaires to handful of Republican presidential candidates, with questions like, “Do you agree with those religious leaders who say that America is a “Christian nation” or a “Judeo-Christian nation?” and what does that mean in practice?”

Criticism of the column revolves around a few grievances.

The first alleges that Keller, in maligning various faith traditions, is encouraging one of the cardinal sins of American life: religious discrimination.

“When I read Bill Keller’s bizarre piece in the New York Times yesterday morning, where he proposes a loaded religious quiz for potential candidates, I actually gasped,” writes Mollie Ziegler, a blogger at the respected religion-in-the-news site Get Religion.

“There must be some deeper meaning here,” she goes on. “There’s no way that the Times would openly display such bigotry or destroy its credibility so thoroughly.

Conservative radio host Hugh Hewitt writes that “Keller's naked appeal to prejudice is startling to me. Can he not know - really not know - how his lines of inquiry play out and how they have always preceded the worst sort of religious intolerance?”

The second, related complaint about Keller's column is that the editor appears to be advocating a loyalty oath from religious candidates, asking them to publicly pledge allegiance to their country over their church.

Though Keller, who was raised Catholic, writes that he was “hurt” and “mystified” when John F. Kennedy faced questions about whether he’d take orders from the Vatican while running for president in 1960, critics say Keller is raising the same sorts of questions about the current Republican presidential field.

The other big gripe is that Keller’s questions are reserved for the Republican candidates; he doesn’t offer a single query for President Barack Obama, even though the electorate remains confused about Obama’s religious faith (most Americans can’t correctly identify the president as a Christian).

Those raising this line of criticism charge that such liberal bias explains why The Times was late to covering the controversy over Obama’s longtime preacher, the Rev. Jeremiah Wright, in 2008. At one point, the controversy about Wright almost sank Obama’s candidacy.

Keller acknowledged such complaints in a tweet on Friday, when his column went up online:

Yes, Dems should be asked about their faith (and influences) too. We were late to Rev. Wright in '08, but we got there, and did it well.

Would be interested in your thoughts on this one. Is Keller raising legitimate questions that much of the news media have neglected, or is his column over the line?