her intention was to make money…..

If I remember correctly Pepsi had a problem with the cross burning in her video and her sexuality, not the song itself.

The highly controversial music video for the song was directed by Mary Lambert, who also directed “Borderline”, “Like a Virgin”, “Material Girl” and “La Isla Bonita”. It was shot at Raleigh Studios in Hollywood, California and Madonna’s scenes with burning crosses were filmed on San Pedro Hills in San Pedro, California. The video featured actor Leon Robinson and premiered on MTV on March 3, 1989, and later went on to win the Viewer’s Choice Award at the 1989 MTV Video Music Awards.

It attracted criticism for its subplot of Madonna making love to Saint Martin de Porres – which some perceived as being a black version of Christ[5] -, its use of Catholic iconography, including a scene where Madonna developed stigmata, and cross burning. The video topped MTV’s countdown of “100 Videos That Broke The Rules” in 2005, and for the 25th anniversary of MTV (August 1, 2006), viewers voted the video as the “Most Groundbreaking Music Video of All Time”. In addition, the video was ranked #20 on Rolling Stone magazine’s “The 100 Top Music Videos” and #2 on VH1’s 100 Greatest Videos. On November 27, 2007 Fuse named “Like a Prayer” as one of its ten “Videos That Rocked The World”.[6]
Pepsi commercial controversy
Madonna was paid $5 million by Pepsi-Cola to appear in a commercial that would predominantly feature the world premiere of “Like a Prayer”. The commercial, titled “Make a Wish”, was filmed at Culver Studios in Culver City, California in late January 1989 and was directed by Joe Pytka. Depicting Madonna drinking Pepsi and watching a home video of her eighth birthday[7], the tone that the commercial sought to convey sharply contrasted with the official music video for the song. When Pepsi executives saw the completed video, they quickly yanked the advertisement after only two airings in an attempt to dissociate themselves from the controversy Madonna had created. (The two-minute commercial was shown just once on March 2, 1989 during The Cosby Show, and, in the UK, after much publicity, on March 2 during a commercial break on ITV 12 minutes into The Bill.)

Though her contract with Pepsi called for three future commercials, Madonna got to keep her five-million-dollar endorsement fee, without fulfilling her contractual obligations. When Madonna won the Viewer’s Choice Award for “Like a Prayer” video at the MTV Video Music Awards in September 1989, in her acceptance speech she thanked Pepsi-Cola “for causing so much controversy!”.

During an MTV interview with Kurt Loder entitled “Breakfast with Madonna” in 1990, Loder asked Madonna about the “brouhaha” surrounding her own video for the song and Pepsi’s reaction to it. Madonna said, “[Pepsi's spokespeople] said they just didn’t like it.”
FROM WIKIPEDIA