Some of the reason's people go away with the perception of AA as a "religious" program.
The constant references to God, and the need to turn your "will and life over to Him". While I understand it is a "God of your understanding", it is still God.
The Big Book is read and poured over very much like the Bible is, with people quoting their favorite passages and oftentimes reading meaning into them that wasn't necessarily there.
The frequent recomendations to "get on your knees and pray" as a method of dealing with issues.
The saying of The Lords Prayer at the end of many AA meetings (at least in the US).
These are just a few of the obvious ones. I'm sure that there are others. I'm also not bringing these up to start an argument, only because the topic was raised and the question was asked. While I personally don't believe AA is a religious organization, it definately has religious overtones. That doesn't make it bad, it is just how it is. It is still a program that has helped and continues to help thousands of addicts and alcoholics. However I think people are putting on blinders when they deny what are obvious religious overtones that make some people uncomfortable. That's about all I have on that. Thanks.