Whether you’re an atheist or a Christian or some other sort of religious believer, there’s a good chance that one day you’ll find yourself in a church or other house of worship with traditions you don’t understand, surrounded by people whose beliefs you don’t share.
That’s especially true at weddings, baptisms, etc., where it’s likely there will be friends and extended family who don’t attend the same church (if they attend any at all). So don’t sweat it too much if you find yourself in such a situation. Even if you’re the only atheist there, you’re not the only fish out of water.
Different churches have different routines. There are sedate churches where the most you have to do is bow your head a few times, or (if you’re feeling ambitious) say some words (or move your lips). Then there are churches that practically give you an aerobic workout — “Everybody stand up! Everybody sit down! Stand up! On your knees!” — and you can feel like an idiot if you don’t know the drill.
(Bonus Power Tip for Protestants: Catholics end the Lord’s Prayer at “deliver us from evil.” If you’re at a Catholic church (maybe for a wedding or baptism) and you pray along with the Lord’s Prayer, and they get to “deliver us from evil” and you go right on with “for thine is the kingdom …” you’re probably going to be the only one still talking. Ask me how I know.)
The good news is, most churches are used to having “foreigners” in their midst, and you won’t get a hard time if you don’t join in. And if you’re still worried about it, you can always ask someone in the main party (the couple getting married or baptizing their kid) about whether there are any protocols you should know about.
This works well whether they know you’re an atheist or not, and whether you want to make it an issue or not. Either way, you’re not from their church and don’t know the traditions, so asking about it is a good way to show concern about making their day special, and/or sending a message that even though you’re an atheist you won’t make a scene when people start praying and stuff. There are lots of good places and times to stand up and be counted as an atheist, but somebody else’s special day isn’t one of them.
Confession time: I got married in a church. Not only married, but counseled beforehand by an Episcopal priest. Fortunately for me, the priest was a guy (the Episcopals let any gender be priests, and they’re even allowed to marry), so there wasn’t a lot of touchy-feely crap about feelings and building relationships and stuff like that. The only part I remember was that he said every man needs a “cave,” and a woman should let him have a place where he can be alone to mess around with guy-type stuff. Whatever. Works for me.
Why get married in a church? Mainly because my wife’s father was very religious and very ill, and it was no skin off our nose for him to see his youngest daughter (and only unmarried offspring) get married in a proper church before he became too ill (physically and mentally) to be there. Was that cowardly of us? Maybe. Would we do it again? You bet.