PBS Discussion - Evolutionary Fact?

I just finished watching the second part of a two-day special on PBS called "The Question of God." On this show there was a panel of brains who sat around a table and talked about video segments that dealt with CS Lewis vs. Sigmund Freud. There was one part of this discussion that bothered me, and I posted about it on the forums that were set up on www.pbs.org to discuss these discussions. Here it is:

I thought this would be a good place to ask this question since it was in the "Love Thy Neighbor" discussion that the comment was made. Here it is:

"And the answer is that in our long evolutionary history of living with a small community of other people, it's not enough to just fake being a cooperator and a good person..."

Okay, here's my question. I listen to the skeptics who are trying to reason away the existence of God, and there is always one underlying theme. In the discussion about miracles, Shermer constantly talked about how truth needs to be observable, and provable, but then he can make a comment like this that just assumes the truth of the evolutionary theory. There is no proof that this process of macroevolution exists or has ever existed, but it is so widely accepted that everyone just assumes that it is true. Where is the proof? What happened to the scientific method? I hope that someone can give me an adequate reply, because it just seems to me that these 'intellectuals' who accuse Theists of using induction in their reasoning are doing the same thing on a larger scale.

Maybe someone reading this can help me out with a reply.