Some of these are actually non-religious, others I'm just interpreting as such. :P
Imagine- John Lennon (This one is a given, I think)
Soul Society- Kamelot "How can we believe in heaven?
Human reason counters all ideas of a soul society
My life is just a fragment of the universe and all
There must be more that I can see"
Dear God- XTC "Dear God, hope you got the letter, and...
I pray you can make it better down here.
I don't mean a big reduction in the price of beer
But all the people that you made in your image, see
Them starving on their feet 'cause they don't get
Enough to eat from God, I can't believe in you"
Hand That Feeds- Nine Inch Nails (This one is supposedly about the war, but the concept applies) "What if this whole crusade's a charade
And behind it all there's a price to be paid
For the blood on which we dine
Justified in the name of the holy and the divine"
The Truth Beneath the Rose- Within Temptation (still a bit religious, but with some good punches at holy wars) "Give me strength to face the truth, the doubt within my soul
No longer I can justify the bloodshed in his name
Is it a sin to seek the truth, the truth beneath the rose?"
This came up on another forum and I posted the same thing. Rush has been athiest inspired lyrics for over 30 years but Neil has definately made it a theme over the last few albums and especially the two new songs so far released on the upcoming album.
The lyric in Caravan, the other song, "In a world lit only by fire" is from the book titled the same by William Manchester and is pretty much a history of the harm religon has done to society up through medieval times.