Ophelia Benson has an excellent, balanced article on the Templeton Foundation in the latest issue of The Philosophers' Magazine. (A paper copy of this turned up here the other day, and I can report that it contains much else of interest, including an interview with Jerry Fodor conducted by Julian Baggini.)
Did I mention that the article is balanced? Yes, I did. Benson is no fan of the Templeton Foundation - far from it - but her piece isn't a hatchet job. It is an exemplary piece of philosophical journalism, exploring the pros and cons of a coontroversial organisation. Would that the same sort of balance could be achieved by all those folks who are currently fawning over Francisco Ayala, now that he's won a huge sum of money for his dubious and philosophically naive views on the relationship between science and religion. One of the evils of the Templeton Foundation is that it can bestow an aura of legitimacy upon very questionable ideas simply by awarding their expositors with a cash prize so egregiously large that journalists are compelled to take notice.
This is the issue in a nutshell. Are philosophy, science and theology different branches of the same kind of inquiry into life and being, which can be usefully and happily united? Or are they fundamentally different kinds of thing, with substantively different ways of inquiring and evaluating the results of inquiry? Templeton clearly considers the first answer correct, while the irreligious tribe of philosophers mostly (but not unanimously) opt for the second. With so much Templeton money hinging on the answer, it could be the $6 million question.
I'm not quite with her on this. I (and probably a lot of other philosophers) actually think that philosophy and science are continuous with each other, and it's not clear where one ends and the other begins. They are part of the larger realm of rational inquiry, and the divisions made within this realm are more practical and pedagogical than anything else.
Theology is a mixed bag. Lot of different and ill-matching stuff gets shoved into theology. Insofar as it includes, for example, rigorous historical-textual analysis of the holy books, it is part of the larger field of rational inquiry. But the core of it is, indeed, something fundamentally different. Still, it can conflict with philosophy and science because it often makes claims that these have the resources to contest.