Many times I have felt that Obama has been speaking about more than one thing with his words. I think this quote in context is meant to be about Global Warming. But in a broader sense, he could have been making a jab at the Bush Administration which he feels did not use facts or evidence in many of their decisions (Federal Marriage Amendment, Iraq, Lack of Environmental Programs). This could most certainly be a nod to those that want our military to stop using "just-war theory"
(applied incorrectly by the Bush Admin I might add) and to those of us who want science to be applied to our legislation on marriage.
It also could have been a political statement with the intention of pro-Gay folks and progressives taking it more broadly and thus making those groups support the President-Elect more whole-heartedly. I'm going to take the glass half-full interpretation right now and hope that Obama employs evidence and facts (and reality) in his decision making on all issues.