I don't think there is one overriding theme. The reason Tolkien created Middle-earth was so that England would have its own mythology, so I don't think it was to tell a message. But when making ME he did put some messages in it. Like the ones mentioned about technology and religion. What Yavanna228 was saying is good, but I see it as not just because of evil, but also, and more importantly, because of time. Nothing can beat time. Time outlasts everything, and Tolkien knew this. He could not finish ME, just as Bilbo could not finish the Red Book of Westmarch. The elves could not withstand time. Yes they may be immortal, but time brings change, and they choose to leave their homes. Anyways, that's what I think.
Here and
here are some other themes, and there are many many more.