The couples' marriage fell apart earlier this year and the 50-year-old actor's obsession with Scientology was blamed for it because Holmes, 33, feared their six-year-old daughter Suri would too become involved in the religion, reported Daily Mirror.
"Now he's lost the most precious thing in his life, he sees that his Scientology beliefs may not have hurt his box office but have ended not one but two marriages.
"It was a terrifying and rude awakening for Tom when Katie served him with divorce papers. He's used to feeling undebatable and untouchable. When he lost Katie he felt a failure," a source said.
Cruise became a Scientologist in 1990 when he was married to his first wife, Mimi Rogers, 56. The end of his second marriage to actress Nicole Kidman, 45, was also blamed on the religion.