Tom Cruise admitted that Katie Holmes filed for divorce because of Scientology. In his deposition, obtained by RadarOnline for his $50 million defamation case against Bauer media (whose magazines claimed he abandoned his daughter Suri Cruise), the actor first exploded with anger when asked if Holmes left him to protect Suri from Scientology.

He said that it was an offensive question, saying "there is no need to protect my daughter from my religion.” Lawyers pushed to ask if his ex-wife ever indicated she left because of the religion or because she wanted to protect their daughter from it. He responded:

"Did she say that? That was one of the assertions, yes."

What's more, Cruise also admitted that his 7-year-old daughter is no longer a practicing member of the religion. This is a huge admission since anyone who leaves the faith is considered a “Suppressive Person” and is cut off from all members of the church, including their immediate family.

People reports:
In the wide-ranging, often contentious deposition, Cruise’s attorney Bert Fields was on hand as the star was forced to answer questions about everything from his use of private jets to Scientology.
He revealed that Suri is no longer practicing the religion. Pressed about whether Holmes left him to “protect” Suri from Scientology, Cruise responded, “I find that question offensive. … There is no need to protect my daughter from my religion.”
But asked whether Holmes left him in part for that reason, Cruise said, “that was one of the assertions, yes. … There are many other aspects to the divorce.”
Cruise also was asked about Scientology’s definition of a “suppressive person,” which includes, according to a definition on the church’s website, those who publicly renounce Scientology and therefore lose “fellowship with the Church as well as with other Scientologists.”
Cruise said that description was accurate, but when asked whether the church would consider Holmes to be a suppressive person, he responded: “That is a distortion and simplification of the matter. I don’t want to just give an oversimplification of religious doctrine.”
He acknowledged that his older kids, Isabella and Connor, whose mom is Nicole Kidman, haven’t had contact with Holmes since the split.
And now that Suri isn't a practicing member of the church, and they've shunned Katie Holmes, she's now considered as a suppressive person.

"According to Scientology doctrine, Katie has denied Suri her spiritual eternity in the church. There's no chance for her now," Domingo explained to Vanity Fair. "Why would Katie deny their daughter her spiritual freedom? How suppressive is that? If [Tom] loves his daughter, he will never give up on [Scientology]. He will try to use every means available to help his child, and he does think he's helping his child, but he's also helping the church control his life."