I do believe that nice religious people make the world safe for extremists by teaching us [...] that faith is a virtue, teaching us that there's something good about holding beliefs without any substantiating evidence. Once you buy into that, [...] then the door is opened to extremists who defend their extremism by saying, 'oh well, it's my faith, you can't touch it, you can't criticise my faith, i don't even need to defend it because faith is faith.'
I do object to the assumption that anything that might be outside of nature is ruled out of the conversation. That's an impoverished view of the kinds of questions we humans can ask, such as "why am i here?", "what happens after we die?", "is there a god?" if you refuse to acknowledge their appropriateness, you end up with a zero probability of god after examining the natural world because it doesn't convince you on a proof basis.
Nowadays theologians aren't quite so straightforward as paley. They don't point to complex living mechanisms and say that they are self-evidently designed by a creator, just like a watch. But there is a tendency to point to them and say 'it is impossible to believe' that such complexity, or such perfection, could have evolved by natural selection. Whenever i read such a remark, i always feel like writing 'speak for yourself' in the margin.