Mysterious Ways is obviously a very religious song.

The first lyric is "Johnny take a walk with your sister the moon, let her pale light in to fill up your room" - this is a direct reference to John the Baptist. The lyrics later state, "you've been living underground, eating from a can, you've been running away from what you don't understand, love"

A lot of people think this song is sexual in nature, especially with the line of "If you wanna kiss the sky, better learn how to kneel, on your knees, boy" but it's actually referencing prayer.

Towards the end of the song, "Spirit moves in mysterious ways" is sung, obviously speaking about the holy spirit. That is who "she" is in the song -- it's the holy spirit.

The line "She sees the man inside the child" is a reference to Mary, Jesus' mother, since she knew of his potential and who he was.

This song does have admiration for women in it, most definitely, since Bono said that it was based on the love of a woman, but it's not as sexual and romantic as most people think it is. It's highly spiritual.