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Cruise has been the face of the church for decades, and as Gibney's film "Going Clear: Scientology and the Prison of Belief" shows, the star allegedly had knowledge of abuses members of the church have endured.
"What a missed opportunity," Gibney wrote in the column. "For once, someone with intelligence, rhetorical skill and insight could have confronted Cruise about the engine of cruelty that drives his chosen religion and reminded the world that the smiling movie star sits idly by, effectively endorsing a longstanding and ongoing pattern of human rights abuses."
The Wrap reported days after the Cruise appearance on "The Daily Show" that Cruise's publicity team enforced a strict no personal questions mandate for access to the star during his publicity tour of "Mission: Impossible - Rogue Nation." That included questions about Scientology.
Instead, Stewart and Cruise discussed workout regiments and plans for another "M: I" movie. Earlier that week on "The Tonight Show Starring Jimmy Fallon," the host had a lip synch battle with Cruise.
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"Part of the problem is the byzantine structure of the entertainment industry," Sophie Gilbert of The Atlantic wrote. "The Daily Show is broadcast on Comedy Central, which is owned by Viacom. Viacom also owns Paramount Pictures, the studio behind the Mission Impossible franchise."
Gibney notes in his column that according to insiders at "The Daily Show," there was no deal to not bring up Scientology.
The filmmaker believes we the audience are also responsible in this.
"We should insist that celebrities play by the rules the rest of us do," Gibney wrote. "And we need to be willing to encourage those who can to ask uncomfortable questions on our behalf."
Read Gibney's complete guest column.
Watch the complete Tom Cruise "The Daily Show" interview: