That's integrity
I'm impressed. Sean Carroll got invited to a conference in honor of Charles Townes with an impressive honorarium ($2000!), and he turned it down. Why? Because it was funded by the Templeton Foundation, and was clearly going to be window dressing for religion.
The point is that the entire purpose of the Templeton Foundation is to blur the line between straightforward science and explicitly religious activity, making it seem like the two enterprises are part of one big undertaking. It's all about appearances. You have a splashy scientific conference featuring a long list of respected participants, and then you proudly tout the event on a separate web page for your program to bring science and religion together.
Not that I have any prospects for being invited to such a well-paid conference, but if I were, I'd have a hard time making that kind of responsible decision. I'd be looking at that pile of tuition bills I'm dreading next year, and then I'd look at the promise of a few thousand dollars for just talking. And the wife would be looking at those bills and giving me that look. It would be so tempting to sell out…but no. Like Sean says,
Religious belief is the Big Lie of our contemporary intellectual life, and scientists more than any other group should be intellectually rigorous about the absolutely real differences between science and faith.
I don't see any difference between the Templeton Foundation and Sun Myung Moon's Unification Church—both are endowed with overflowing buckets of money and a dearth of reason, and are pouring that cash into efforts to subsidize public insanity.


I dunno. Although I am an atheist, and I recognize the destructive power of most religion, denouncing the Templeton Foundation seems like saying "not only am I an atheist, but I refuse to have any theist friends." If people of good conscience can believe in God, why not accept an honor from a religious organization?
When it comes to blurring the line between science and religion, I think it all depends on what you mean by “religion.” (Science is well defined: religion is not.) We North Americans tend to draw our picture of religion from a very narrow range of religious practice: we think of the big monotheisms, Christianity, Judaism and Islam. As a result, we assume that either faith or belief in an infinite being or both is necessary for religion. But the Greek gods were quite finite. Many forms of Buddhism lack a creator god all together. (In general I’ve found that Theraveda Buddhism, which sticks closest to the original texts, has the least amount of weirdo metaphysics.) The whole idea of belief on faith is basically a product of early Christianity. Its really a local aberration.
Because science is a well defined enterprise and religion is not, the templeton people mostly succeed in expanding our notion of what counts as religion ("progress in religion" what an odd phrase.) This strikes me as a good thing.