Ebert is specifically mentioned as an atheist in this recent article:
From Esquire (February 16, 2010)
"He begins to write about more than movies; in fact, it sometimes seems as though he'd rather write about anything other than movies. The existence of an afterlife, the beauty of a full bookshelf, his liberalism and atheism and alcoholism, the health-care debate, Darwin, memories of departed friends and fights won and lost — more than five hundred thousand words of inner monologue have poured out of him, five hundred thousand words that probably wouldn't exist had he kept his other voice.
Ebert is dying in increments, and he is aware of it.
I know it is coming, and I do not fear it, because I believe there is nothing on the other side of death to fear, he writes in a journal entry titled "Go Gently into That Good Night." I hope to be spared as much pain as possible on the approach path. I was perfectly content before I was born, and I think of death as the same state. What I am grateful for is the gift of intelligence, and for life, love, wonder, and laughter. You can't say it wasn't interesting. My lifetime's memories are what I have brought home from the trip. I will require them for eternity no more than that little souvenir of the Eiffel Tower I brought home from Paris.
There has been no death-row conversion. He has not found God."
From Roger Ebert's 14-Jun-2002 review of "13 Conversations About One Thing" ...
"The truth hidden below the surface of the story is a hard one: Nothing makes any sense. We do not get what we deserve. If we are lucky, we get more. If we are unlucky, we get less. Bad things happen to good people and good things happen to bad people. That's the system. All of our philosophies are a futile attempt to explain it. Let me tell you a story. Not long ago, I was in the middle of a cheerful conversation when I slipped on wet wax, landed hard, and broke bones in my left shoulder. I was in a fool's paradise of happiness, you see, not realizing that I was working without a net--that in a second my happiness would be rudely interrupted.
"I could have hit my head and been killed. Or landed better and not been injured. At best, what we can hope for is a daily reprieve from all of the things that can go wrong."
"And yet, even so, there is a way to find happiness. That is to be curious about all of the interlocking events that add up to our lives. To notice connections. To be amused or perhaps frightened by the ways things work out. If the universe is indifferent, what a consolation that we are not."
From his review of Mel Gibson's Passion of the Christ, Ebert says:
It is a film about an idea. An idea that it is necessary to fully comprehend the Passion if Christianity is to make any sense. Gibson has communicated his idea with a singleminded urgency. Many will disagree. Some will agree, but be horrified by the graphic treatment. I myself am no longer religious in the sense that a long-ago altar boy thought he should be, but I can respond to the power of belief whether I agree or not, and when I find it in a film, I must respect it.
Somewhat relatedly, in a March 28, 2005 commentary  Ebert fiercely defends the rights of moviegoers to see films which mention biological evolution. At the time, protestors had successfully prevented the showing of 'Job vs. the Volcano' at some IMAX theaters in southern states. He makes the case that science and religion need not be in conflict over evolution as each inhabits its own realm. This position is very similiar (if not identical) to Stephen Jay Gould's "Non-Overlapping Magisteria (NOMA)" . Though Gould regarded himself as agnostic, NOMA is accepted by many non-believers and believers.
I know it is coming, and I do not fear it, because I believe there is nothing on the other side of death to fear. I hope to be spared as much pain as possible on the approach path. I was perfectly content before I was born, and I think of death as the same state. . .
My opinions have been challenged. I had to defend what I believed. I did some more reading. I discovered fractals and Strange Attractors. I wrote an entry about the way I believe in God, which is to say that I do not. Not, at least, in the God that most people mean when they say God. I grant you that if the universe was Caused, there might have been a Causer. But that entity, or force, must by definition be outside space and time; beyond all categories of thought, or non-thought; transcending existence, or non-existence. What is the utility of arguing our "beliefs" about it? What about the awesome possibility that there was no Cause? What if everything...just happened?
I was told that I was an atheist. Or an agnostic. Or a deist. I refused all labels. It is too easy for others to pin one on me, and believe they understand me. I am still working on understanding myself.
Go gentle into that good night By Roger Ebert on May 2, 2009 11:27 AM