Some insiders have suggested the answers may be found in the actor's childhood.
Cruise first revealed his abusive childhood in 2006, when he spoke of his father, Thomas Cruise Mapother III, as a "bully and a coward -- the person where, if something goes wrong, they kick you. ... It was a great lesson in my life, how he'd lull you in, make you feel safe and then, bang!"
In an interview with Parade magazine just before Holmes gave birth to their daughter Suri, Cruise said about his childhood years with his father, "For me it was like, 'There's something wrong with this guy. Don't trust him. Be careful around him.' There's that anxiety."
The actor was 12 when his mother left his father, taking Cruise and his sister Lee Anne with her.
The next time Cruise saw his father was 10 years later, when Mapother "was in the hospital dying of cancer, and he would only meet me on the basis that I didn't ask him anything about the past," the actor said.
"When I saw him in pain, I thought, 'What a lonely life.' He was in his late 40s. It was sad," Cruise told Parade.
Now 50, Cruise could be facing a similar loneliness without Holmes, his third wife.
Speaking out for the first time since she signed the actor at 18, Cruise's former manager Eileen Berlin, says she wasn't surprised when his marriage to Holmes failed.
"He just couldn't have a relationship and I think that was because you have to open yourself up and he'd been too hurt by his father to do that," Berlin told the UK's Daily Mail.
"The world sees this good-looking guy, worth millions. I still just see this little boy," she said.
Though his longtime attorney Bert Fields said in a statement about the settlement reached Monday between Cruise and Holmes, "Tom is really pleased we got there, and so am I," the actor was initially reeling by Holmes' decision last week to file for divorce.
Sources close to the actor told ABC News that Cruise was "stunned" by Holmes' action, which his publicist said left him "deeply saddened."
He returned to Los Angeles from filming in Iceland last Tuesday to celebrate what was described as a "somber" 50th birthday celebration with his family, including his two older children, Connor and Isabella, both of whom he adopted with wife Nicole Kidman.
A settlement with Holmes was worked out quickly and quietly and, according to Holmes' lawyers, "amicably." Insiders said the focus was first and foremost on Suri and just before it was announced that Cruise and Holmes had signed an agreement, they released a joint statement, saying:
"We are committed to working together as parents to accomplish what is in our daughter Suri's best interests. We want to keep matters affecting our family private and express our respect for each others commitment to each of our respective beliefs and support each other's roles as parents."
It appears that Cruise could be committed to giving his daughter the childhood he felt he didn't have.
"I had no really close friend," he told Parade about his school years. "I was always the new kid with the wrong shoes, the wrong accent. I didn't have a friend to share things with and confide in."
The actor has said he harassed by his classmates while he was growing up.
"So many times the big bully comes up, pushes me. Your heart's pounding, you sweat, and you feel like you're going to vomit," he recalled to Parade. "I don't like bullies."
For years, Cruise also carried around the shame of being diagnosed with dyslexia.
"The school took me to a psychiatrist to get tested," Cruise told the magazine. "They said, 'Oh, he's dyslexic.' I'm labelled. It instantly put me into confusion. It was an absolute affront to my dignity.
"I remember thinking, I've got to figure this out. What's normal? Am I normal? Who's to say what's normal? I didn't understand what 'normal' is. It still doesn't make sense," he said.
In contrast, Holmes' childhood seems downright sunny. The youngest of five siblings, Holmes had a Catholic upbringing in Toledo, Ohio, where she attended the all-girl Notre Dame Academy. She appeared in the school musicals "Hello, Dolly!" and "Damn Yankees" before being cast in Ang Lee's "The Ice Storm," followed by her breakout role in "Dawson's Creek."
And like so many girls her age, Holmes had posters of famous heartthrobs on her wall, including one of Tom Cruise. Months before she and Cruise started dating, she confessed to Seventeen magazine in October 2004, ''I used to think I was going to marry Tom Cruise.''
The rest, as they say, is history.