I've always thought that the meaning of this song was quite evident...
I mean to me it's all about the need of peace and yes,of course there are many reasons for one to reach out for peace,i personally don't know what Jon was looking for.
It's such a positive song,when i listen to "up the steps of the church,through the fields,in the dirt,in the dark I have seen that the sun still shines for the one who believes" i just feel better...