It's obvious, isn't it. He's not getting to spend time with Suri, his little girl with Katie Holmes. 

A source spilling all their beans to Star Magazine (via HollywoodLife) had this totally plausible scenario as to why Tom Cruise may abandon his beloved Church of Scientology. The ball started rolling in Cruises' brain after a phone call with his now nine-years-old...

"She was going on and on about her ballet class and how much she loves it. That’s when Tom realized he’s never seen her perform ballet and he started to tear up. It hit him that she's growing up before his eyes and he’s not there to witness most of it. They talk on the phone and video chat, but it’s not the same... Tom has been under tremendous pressure where Suri and Katie are concerned because the church doesn’t want him close to them. They can't stand that their own poster boy isn’t raising his child in the church... If they label Suri a suppressive person (a Scientology term for an enemy of the church), as they’ve been known to do with dissenters, that would make it hard for Tom to have a relationship with her. He’s between a rock and a hard place, but he’s finally making a choice to put his daughter first."
One thing's for sure, Tom Cruise's departure from the Church won't be a quiet one. Although, Katie and Tom's divorce did happen in a remarkably swift and shushed fashion...

 

Via Uproxx