Over the past few years I've observed the Templeton Foundation with some bemusement, as it seems to sponsor all sorts of things that seem interesting-but-bordering-on-flakey. I don't have a problem with its general goal, which to explore the connections between science and religion. As a moderate in the God wars I'm all for people trying to find a middle way.
So, I was a bit disturbed to find out that a boatload of Templeton money is going to the forces behind California's regressive Proposition 8, which would strip away the rights of gays to be married (rights they gained under a recent CA Supreme Court decision). John Templeton (son of the founder of the Templeton Foundation and its current chairman) has contributed $1 million dollars to a collection of groups campaigning for this odious law (along with Howard Ahmanson, another crazy rich guy who funded the similar but less respectable Discovery Institute).
Templeton funds many interesting scientific and quasi-scientific efforts, including the Foundational Questions Institute, which lists many prominent people as members and affiliates, including science bloggers Scott Aaronson and Sean Carroll.
I don't think there is anything inherently wrong with taking money from the Templeton Foundation, no matter what dubious causes they may be linked to. Money they spend on actual research is money not being spent on supporting regressive legislation. However, if I was taking money from such people (and I have been in somewhat similar situations, where I've accepted military funding for my own research), I would feel some extra obligation to speak out for goodness, righteousness, and truth in areas where my patron is spreading evil, hatred, and lies. Just saying.
On the intellectual level, I'm disappointed to learn that Templeton-brand religion is the fundamentalist/wingnut variety -- the kind of God that hates teh gay, not the kind of abstract principle of existence and value that an intelligent person might conceivably have truck with; not the unnameable of mysticism or apophatic theology; no, this is a God with very firm opinions about the proper deployment of human genitalia. There are sane people who work on reconciling science and religion, but they apparently have no crazed billionaires behind their efforts.