Morality and religion; two things that are only the same when it comes to those who strictly believe in their religion. I, however, stand with Rustin N in saying that they are completely, beyond a shadow of a doubt, different.
There are people that do the right thing because they fear what may come if they don't (i.e. burning in Hell forever). There are also people who do the right thing because it is the right thing to do, not because some deity will unless all his/her wrath upon them.
This is the flaw of religion. It somewhat forces people to do things and to believe in this and that, lest all hell be unleashed. For example, many followers of the Bible believe that homosexuality is wrong; a large portion of those people think this because they are told to. There are no moral beliefs that shape this opinion. An atheist, on the other hand, might think that homosexuality is wrong simply because it is wrong.
I'm not saying to shun religion and those who follow it and go around town burning every Bible in sight - rather, make your own beliefs. If something is wrong, make sure it is wrong because you think it is wrong, not because a magical almighty being does.