Morals exist as part of the human condition not as a product of religion. Humans are social animals that live in groups. Like any other group animal we developed certain traits which allowed us to live together in relative harmony. We certainly would not have made it far as a species if our ancient ancestors were nihilistic murders. In short we do not kill each other for the same reasons a band of monkeys do not kill each other.
Religion on the other hand creates their own moral code which exists solely within the confines of their own religion. For example sex before marriage may seem immoral to a fundamental Christian but marriage itself is an idea created by man. It has no meaning outside the confines of that religion’s particular beliefs.
Personally I believe that it is immoral to unjustly persecute someone. Homosexuality is a completely natural phenomenon just as heterosexuality is and occurs in countless species. Now it would seem pretty odd to persecute someone for being a homosexual but some religions do so on the grounds that it is a sin. A sin? According to whom? Well their own religious code, of course. So now we have the odd case where a group which claims to have moral superiority commits immoral acts and convinces themselves that this immoral act is somehow virtuous.
Religion didn’t invent any of the real moral codes, they are innate. As for the rest (don’t eat shellfish or pork, work on Sunday, etc), that is just a bunch of extra stuff they made up along the way.
In closing, there is no reason why an Atheist would be less moral than a religious person. In fact, since they are not saddled with many of the odd and often conflicting notions religion introduces they are probably less likely to commit an immoral act out of confusion or a misguided sense of right.
