I guess it depends on how you personally define religion. I know some people look at religion as the belief that a series of practices/rituals are necessary, or perhaps the belief that you have to do certain things in order to be saved. From that perspective, I can see why someone might be against 'religion'. There was a picture I once saw that said something like, "Religion says, "Do." God says, "Done!"" We can argue about that sort of stuff, I suppose, or agree that salvation is through faith in Christ alone. Personally, I prefer the latter.
Anyway, there are four '3' songs that come to mind that I'm not particularly sure how to take. If you don't mind having a look at the lyrics and telling me what you think, I'd appreciate it. I'll link to them, and try to give you an idea of what I'm unsure of.
Halloween
The part that makes me unsure is the "Deeper, deeper than God" part. I think I read that the song is supposed to be about an angel and a demon arguing over a sick boy or something. I believe it was in the liner notes for the album... I'd have to dig it out to be sure, but I think that was supposed to be the idea.
Rabid Animals
The lyrics that make me wonder here are: "And so we pay the price/For having sliced and diced/We nail our Jesus Christ/To the wall". The rest of the song doesn't seem to even mention anything having to do with Christianity/religion in general, so I wonder if the use of Jesus' name here isn't meant to be symbolic.
One with the Sun
Honestly, just the song in general. I actually think it's supposed to be about Jesus' crucifixion, just told in an abstract way, especially with lyrics like, "Started with the sequel so we knew who you would kill", "All the crazy people/Are gathered on the hill/Sharpening the steeple/For the blood they're going to spill/But they are what they kill" (The whole reason the Pharisees wanted to kill Jesus was because they felt he was blaspheming, right? Therefore, in killing him, they are the true blasphemers, hence "They are what they kill"), and "It's time tables turned on Babylon". I'm just not sure if I'm reading too much into this, or if it is supposed to be about Jesus' crucifixion and that's it, or if there's some other meaning here.
Amaze Disgrace
This one... I think it's just the title more than anything. I honestly can't figure out what the lyrics are supposed to be about. If you can, then kudos.
I also read an interview with their frontman (who I think writes most if not all of their lyrics) where he stated that his original bassist and guitarist left because he wouldn't commit to being a 'Christian' band, because it wasn't his thing. He said that he didn't have anything against Christianity, though, and that the guitarist ended up coming back after having a spiritual vision or something like that. Well, the only part of that with any relevance to this is that he doesn't have anything against Christianity...