The line is telling Christians to stop treating God like he is in a box and to treat God like He has limits. Some Christians talk about God like they know exactly what His purpose was for world events or any events, too. The song tells Christians to "get out from under their beds" and actually do something instead of being so passive and just putting their heads in a Bible at home, go to church on Sundays and that's it. It's a song asking them to do more in the world - probably connected to Bono's work in Africa.
This is one of my favorite lines from Bono. I really think it is saying to church people to stop spreading the word of God to non-believers or the rest of the world like it's something that can be kept inside a box. It's telling them to stop talking about God in a fake, timid, almost patronizing way. It's about Christians and church people getting in the way of God or religion getting in the way of God implying that God has no borders or limits and often times is not in the places where some people might expect Him to be (church, for example).