After linking to this article on Facebook, I was challenged to explain how an atheist could justify the respect for life that Jillette calls for, if life is just "meaningless, animated matter." This gets at the heart of the perennial question of how atheists can justify their ethical code.
I can't speak for Jillette, not knowing much more of his particular worldview than what was in the article linked above. Certainly there are people whose atheism leads them to see life as "meaningless, animated matter" -- and those people can very well end up either cynical nihilists or in deep denial. (Then again, there are plenty of theistic cynical nihilists -- after all, what is more cynical or nihilistic than Pascal's Wager?) I, however, do not take such a dim view of life. I think that life creates its own meaning -- indeed, the capacity to do so is one of the criteria for sentience. And the ability to create one's own meaning is pretty awesome, amazing, and respect-worthy thing. My own life, for example, is meaningful to me because I have worked out for myself what purpose(s) I want it to serve, and taken responsibility for that. A view that makes meaning entirely dependent on God is one in which we respect life because an outside party is telling us "do this or else," or "don't break my stuff." We might go through the motions of respect, but that respect is not really premised on the intrinsic value of the things we're respecting.
That being said, I think "respect" is a pretty fuzzy concept. What exactly does it mean to "respect" something? The best definition I can come up with right now is that respect involves fully recognizing -- not just giving intellectual assent, but really grokking -- the facts about the thing being respected. We respect the dangerousness of a fire, for example, when our actions show that we really understand how fires burn and what kind of pain we'd be in if we touched it. (This is not to say you can't touch it, any more than respecting nature would mean walling it off as a pristine wilderness -- you just have to make that decision with full awareness of the consequences.)
One of the facts about life is that living things (or at least sentient ones, which are what I'd apply Jillette's "respect for life" principles to) care about what happens to them and their world. If you truly respect someone, then you have to fully take into account that fact. To count someone else's desires as mattering less than yours simply shows that you don't really recognize the existence of their desires. It would be like if I said Ginger Hill (1440 feet above sea level) is taller than Mt. Everest (29,000 feet above sea level) because Ginger Hill's feet count more -- you'd say I didn't understand the whole concept of feet as a measuring unit. We have, then, a perfectly good (broadly utilitarian) foundation for ethics without needing to invoke God (albeit also without needing to deny her existence, either).
*Bad philosophy collapses in on its own internal contradictions. Good philosophy allows you to see beyond its author's own assumptions and prejudices.