Stone is an Emmy Award-winning American screenwriter, producer, voice artist, musician and actor, best known for being the co-creator of South Park along with creative partner Trey Parker. 
The Onion: Is there a God?
Trey Parker: Yes! Absolutely.
O: Do you believe in more of a nebulous spirit world, or a big man in the sky?
TP: Wow, you know, this would be an eight-hour conversation, and you'd have to get me a little more drunk. I can explain exactly what's going on, but I need to be a little more drunk. I really do have it figured out. I figured it out about a year ago, and it's great. It's all good. We're fine.
O: But the central thesis is that there is a God.
TP: No. There's a God, and there's also this table, and it's the same thing.
O: Matt Stone, is there a God?
Matt Stone: No.
TP: Oh, there's also a God, and his name is Prince.
In the commentary for the South Park episode Go God Go, which features Richard Dawkins, Stone talks about how they have been wrongly perceived as atheists. He paraphrases an interaction he remembers in their Nightline interview:
Interviewer: So, you guys are atheists?...because you've made fun of religion a lot on the show.
MS: What? No. We're not atheists." 
During an October 14, 2004 NPR interview on Fresh Air NPR interview, Stone stated:
"I'm Jewish simply because... my mom is Jewish... but... I grew up completely secular and completely agnostic... I am the worst Jew in the world. I know nothing about the religion. I'm completely agnostic (my poor mother)." 
However, Stone has obviously had a shift in his thinking, as is revealed in a recent article, "Trey Parker and Matt Stone Talk About Why 'The Book of Mormon' Isn't Actually Offensive and the Future of 'South Park'", by Vulture on 3/11/11:
Stone: "We’re essentially atheists — I mean, I am; Trey I don't want to speak for. But coming from that point of view, we’re atheists who don’t hate religion, who are kind of fascinated by it and kind of admire it. [We thought], What would that look like? What would an atheist love letter to religion look like? And I think that’s what this musical is. Now, I don’t think that every Mormon will necessarily like what this love letter says, but it’s our version of, “Hey, we think religion is really cool, here’s what we think about it.” And it’s a musical, so it’s gotta have a feel-good end, and it’s gotta have a big heart, a big story. And that’s the only way to really tackle talking about religion in narratives, is treat the people in them like really good people who are trying to do the right thing. Instead of like, “Look what they do at the tip of a gun, fucking religion.” That’s like, you’re obviously not interested in having a real discussion about it. And that wouldn’t be a very fun musical to watch."