[4] Much of Flynn's work addressed church-state issues, including his 1993 book The Trouble with Christmas, in connection with which he made hundreds of radio and TV appearances in his role as the curmudgeonly "anti-Claus", calling attention to what he viewed as unfair treatment of the nonreligious during the year-end holiday season.

He contributed a new Introduction to A History of the Warfare of Science with Theology in Christendom by Andrew Dickson White[6] and blogged on The Washington Post's On Faith site during 2010 and 2011.

Reading Ingersoll's florid Gilded Age speeches in defense of agnosticism and atheism confirmed him in his identity as an atheist and kindled his desire to become a public activist for unbelief.

[10] The book received ongoing media attention; in 1994, Flynn was the only on-screen expert in A&E Network's first Biography segment on Santa Claus who was not a Greek Orthodox priest.

Galactic Rapture, published in 2000 by Prometheus Books, concerns the rise of a consciously fraudulent false messiah on Jaremi Four, a ruined, quarantined world.

Undercover documentarians from the galactic empire to which Earth belongs (human cameras known as Spectators) present the false messiah's story to eager audiences on many worlds.

Defying the ruined planet's quarantine, a corrupt mining magnate, a bumbling Mormon televangelist, and conspiring Catholic cardinals doing the bidding of the Pope jockey to establish influence on Jaremi Four and claim a piece of the alleged next Christ for themselves.

It features the Mormon comic villain from the first novel; Gram Enoda, a young Earthman on the make who has accidentally acquired a hugely powerful, self-aware digital assistant, and a darkly charismatic televangelist whose theology is drawn from 19th century German and Russian nihilism who wind up interfering in a top-secret government plan to quite literally save the Galaxy.

[20][21][22] In 2007 Prometheus Books published The New Encyclopedia of Unbelief, an 897-page reference work on atheism, agnosticism, humanism, and related philosophies edited by Flynn.

Intended as a successor to the 1985 The Encyclopedia of Unbelief edited by freethought bibliographer Gordon Stein, the work earned mixed reviews.

The International Review of Biblical Studies praised it, saying, "This is a most valuable addition to all existing encyclopedias of religion because it offers the calmly argued perspective of contemporary freethinkers, atheists and secular humanists".

[23] Atheist blogger Santi Tafarella criticized the work's choice of topics and its pre-Internet approach to its subject matter, but still finds the book useful.

[24][25] Flynn is executive producer for American Freethought,[26] a TV documentary series on the history of secularism and censorship in the United States.

Flynn designed the freethought museum at the birthplace of 19th century agnostic orator Robert G. Ingersoll in Dresden, New York, and has been its director since it opened to the public in 1993.

CODESH Inc., as the Council for Secular Humanism was then known, purchased the property for $7,000 and pressed successfully for its inclusion on the National Register of Historic Places.

Though Flynn was employed at CODESH during this period he was not closely involved with the purchase and rehabilitation, which were orchestrated primarily by chairman Paul Kurtz, then-Free Inquiry editor Tim Madigan, and colleague Richard Seymour.

Grothe on Point of Inquiry "He [Ingersoll] literally was seen or heard by more Americans than would see or hear any other human being until the advent of motion pictures or radio.

[36] The secularist movement should emulate the strategies employed successfully by LGBT activists in recent decades, especially publicizing its numbers and encouraging nonbelievers to "out" themselves.

Before the emergence of same-sex marriage as an attainable reform goal, LGBT activism seemed more likely to compel the creation of a wholly secular civil union system that would have provided an alternative to traditional matrimony and would probably have seriously undercut it; in the long term this is a more desirable goal than simply expanding traditional marriage to include same-sex couples.