The arguments for and against Shermer writing for Templeton brings to mind the work of Leni Riefenstahl, and how it is so tainted because of who the financers and supporters were. I am not suggesting an equivalency, but there is a slippery slope when one does work for organizations that are wholly focused on propaganda.

Clearly, Templeton is not the Nazi party. But when Riefenstahl did her filming of the Olympics, the Nazi Party was not yet iconized as the ultimate evil. Not everyone disagreed with the Nazis in 1936, including Henry Ford, Charles Limburgh, Herbert Walker (father of Prescott Bush), Prescott Bush (father of George Herbert Walker Bush), and many other capitalists and high ranking members of the Republican party (who coincidentally had just tried to overthrow the government of the United States in 1934 until their plot was outed by Smedley Butler).

Consider this writeup of her film on the 1936 Olympics

In 1936, Hitler invited Riefenstahl to film the Olympic Games in Berlin, a film which Riefenstahl claimed had been commissioned by the International Olympic Committee. She also went to Greece to take footage of the games' original site at Olympia, where she was aided by Greek photographer Nelly. This material became Olympia, a successful film which has since been widely noted for its technical and aesthetic achievements. She was one of the first filmmakers to use tracking shots in a documentary, placing a camera on rails to follow the athletes' movement, and she is noted for the slow motion shots included in the film. Riefenstahl's work on Olympia has been cited as a major influence in modern sports photography. Riefenstahl filmed competitors of all races, including African-American Jesse Owens in what would later become famous footage.

Riefenstahl could rightly claim that this work was about Olympics and athletics, and not a an endorsement of an evil empire. But since the Nazis used it as propaganda, one cannot watch this film without a sense of horror, because one knows the ultimate history of the promoters of this film.

Shermer being paid by the Templeton Foundation has this same nuance. Suppose you knew that in 10 years, some simpleton relidiot (Sarah Palin comes to mind) championed and promoted by the assets of the Templeton Foundation takes control of the US Military, and fulfills the failed mission of the 1934 capitalists. The capitalists get the assets and the feudalism they prefer, and the relidiots get to enact Christian Sharia, backed by a nuclear arsenal.

Supposed that the New Christian Theocracy party has a vision that it is God's devine law that Armageddon be visited on the Middle East in fulfillment of prophacy. Millions are dead and tens of millions more dying from radiation and social fabric destruction.

Doesn't implicit support of organizations whose commitment to propaganda over reason create or further the potential for such catastrophic outcomes?

The difference between Shermer and Riefenstahl is that Riefenstahl did support, and was enamoured by the Nazi party, and Shermer claims no affection for Templeton, other than their money. But that is an irrelevant distinction when events go awry, and those in control of the message turn out to be far more evil and destructive than imaginable.

Again, I refer back to what a majority of people, inside and outside of Germany thought about the Nazis in 1934. Most had no idea of how different things would be in 1945.