Before you get excited, the short answer is
I don’t know for sure I would be suprised if he wasn’t. Everything you read here is speculation based on publicly available information.
That being said, I suspect the answer is “yes”. The quote that gave me this impression comes from an interview (emphasis mine):
The thing about playing gods, whether you’re playing Thor and Loki or Greco Roman gods or Indian gods or characters in any mythology, the reason that gods were invented was because they were basically larger versions of ourselves.
Another indication is that while he constantly talks about how much of a privilege it was to work with great actors, and how glad he is that he got the opportunity to do movies like The Avengers, he never mentions or thanks god. Perhaps these practices are only common in America? Though, he has responded “bless you for saying that” in response to compliments.
In this interview, he went out of his way to affirm that he is fine with homosexuality — something most religious people probably wouldn’t do. The interviewer asks if he is metrosexual and he responds:
Um.. m- m- I.. maybe hetero? I d-definitely hetero, I would say. Yeah. Em. <giggles> But that’s just my particular preference. I have nothing against metro, or anything else, for that matter.
So, why would he have never mentioned being an atheist? My guess that it’s still early enough in his superstardom that he is concerned about alienating his fanbase. Especially in the super-religious US.
He read classics at Cambridge University. That environment would have exposed him to ideas and peers that make it hard to continue believing in a god — if he ever did. Atheism has been reliably shown to be correlated with intelligence. He’s seems to be an intelligent, thoughtful person. Given that and the quotes above, I think he’s likely an atheist.
This last quote from Tom doesn’t indicate much, but it is a lovely secular humanist sentiment:
I think if I had anything that I would like to leave behind as sort of a message, I’d want people to understand the primacy of kindness. The power of it to change the world. [source]
Do you have any evidence one way or another? I’d love to hear it.
Edit (9.18.2012) – Found two quotes possibly showing Tom believes in god:
I try not to make plans. God always laughs at your plans.
The other, from his twitter account, dated 25 Oct 11, is him quoting Chariots of Fire:
I believe God made me for a purpose, but he also made me FAST, and when I run, I feel his pleasure.
Though, this last may just be an expression of how he feels about running. Loon.
Edit(2.6.2013) – Thanks to reader Sophie mentioning the “Manifesto for Atheists” — Tom has apparently posted a link to this recently. This is sufficient evidence for me!