That's a pretty lofty confusion to make isn't it? Let's look at the chorus for an example:
When you call my name it's like a little prayer
I'm down on my knees; I wanna take you there
In the midnight hour I can feel your power
Just like a prayer, you know I'll take you there
The chorus is a big bundle of confused meaning that is very interesting, but for now notice simply who the actor is in each phrase. The line "In the midnight hour I can feel your power" obviously implies that God (or perhaps a lover) is the actor, Madonna simply feeling His effects either way. The following line, "Just like a prayer, you know I'll take you there," reverses the power dynamic. Now Madonna is the actor. She is in the "God" position. The first two lines do a similar thing. While "When you call my name, it's like a little prayer" could be understood as God calling Madonna (as in the first stanza—"I hear you call my name"), the phrase "it's like a little prayer" allows one to interpret the lyric as saying that when people call her name it is like they are praying to her. That power position reverses in the second line with the image of Madonna praying "I'm down on my knees" and then switches again with, "I wanna take you there."
So what's going on? Who is praying to whom? Because these reversals continue until the bridge section of the song (beginning "Just like a prayer, your voice can take me there") it seems that the most likely answer is that Madonna is punning on her own given name, on purpose. In Roman Catholicism, the Blessed Virgin Mary, who is also called "Madonna" ("my lady" in Italian), is highly revered. Because people pray to the Blessed Virgin Mary, calling Madonna's name ("When you call my name") would indeed be "like a little prayer."
But once again, that is a lofty pun if ever there was one. It does accomplish something though. The puns and reversals aid Madonna in confusing the erotic and the religious. But first let's take a look at the general idea of sex and religion, in particular as it applies to this song. In his essay "Like A Critique," cultural scholar Stephen E. Young does a good deal of explaining with regards to the odd couple (he gets fancy and says "dyad" instead) of sex and religion:
"We long for, desire, the single in sex; contemporary love songs are filled with lyrics calling for a relationship that will last 'for the rest of your life' (Chicago), or 'Is this the eternal flame?' (The Bangles) and so on. We also long for the single in religion: 'I am the Way, the Truth, and the Life; no man cometh unto the Father but by me' (John 14:6). ... Conversely, we fear the multiple—in sex and religion. And that fear is reinforced by many things that are happening in the world around us."
No doubt what Young speaks about with regard to fearing the multiple in sex and faith are connected in religion. Marriage, though it often does not fulfill its promise "til death do us part," might be seen as a manifestation of the assurance we find in the single. So, sex and religion seem to make sense together if you aren't too offended by the very idea of the two. But what does it mean to blend sex and religion, in the sense that Young was thinking of when he justified their "dyadic" pairing. Let's go straight to the source, "Like A Prayer."
It is totally justifiable to find "Like A Prayer" singularly about religion after a couple of casual listens. The imagery is all there: "angel sighing," "I close my eyes, oh God I think I'm falling / Out of the sky," "Heaven help me," "Let the choir sing," etc. But a closer listen finds some of the lyrics sexually charged. The phrase "In the midnight hour" in the chorus is totally sexual, or at least it could be. With Billy Idol's "Rebel Yell" ("In the midnight hour, / She cried more, more, more") and Wilson Pickett's "In the Midnight Hour" ("That's when my love comes tumblin' down") there seems to be no question. But so far we've only got juxtaposition of sex and religion. The real blending of sex and religion comes from the double meaning implied in each line. Does "It's like a dream, no end and no beginning / You're here with me; it's like a dream" imply romance or spirituality? Or, from the chorus, "In the midnight hour I can feel your power / Just like a prayer." Is Madonna praying in the middle of the night or is the power here a sexual one? When she says "You know I'll take you there" what does she mean? Is the destination the heavens above or a kind of erotic ecstasy right here on earth? On top of this, the entire song is related through simile, everything is "like" something else, which suggests that religion is being used as substitute imagery for something else entirely. It's more than a hidden double meaning; religion and sex seem hopelessly entangled here, just as Madonna and the Blessed Virgin Mary become entangled through pun.
Returning (finally) to the pun, and how it lends itself to the sex/religion pairing, the pun creates a sense of duality in the song. That is, where praise songs typically sing to the (singular) Father, "Like A Prayer" has two interchanging subjects of prayer—or something like prayer. There is the standard male figure, and then there is Madonna. Each seems equal. Going back to the chorus, each worships the other. Madonna with "In the midnight hour I can feel your power" and the male figure with "When you call my name it's like a little prayer." Visually, there is a sense of two equal figures "praying" to each other, becoming spiritual beings through their mutual interactions. If this is sex, it makes a little more sense.
From the feminist perspective, Madonna's use of pun—in conjunction with her pairing of sex and religion—is a mechanism for female empowerment. On the conventional, sexual level, Madonna establishes herself as an equal to whoever she's with. And on the level of religion, Madonna challenges the established patriarchy by placing herself, as a woman, with God.