It's because the raw box office take tells only a small part of the story.
In general a studio only gets about half the domestic take, a little less than half of the international take. It varies from picture to picture, year to year and so forth but the rule of thumb is probably pretty good. The money the studio doesn't get goes to the theaters, the theater chains, distributors, and all the other people between the movie studio and your theater seat. We'll leave the discussion about how accurate all these box office numbers being released by studios and posted on the Internet are (especially the foreign numbers) for another thread.
The other issue with 'Pearl Harbor' was the enormous cost. The "negative cost" the cost to complete the negative from which copies of the final film are made was over $150 million. At the time it was the most expensive movie ever made by a single studio ('Titanic' was split between Paramount and Fox). Because the movie cost so much, Disney launched a massive marketing campaign to "ensure" its success. At the time too, 'Pearl Harbor' had the greatest "awareness factor" (i.e., people knew that the movie was coming to theaters) of any movie ever tested. But it came at a price; most of the rumors estimate that between $80 and $95 million was spent on the campaign. Disney even spent $5 million to host a premier party onboard an aircraft carrier anchored in Hawaii.
Even bigger costs don't show up in the numbers at all. To keep the initial cost down, many of the "big names" involved with the movie agreed to a low up front salary for "points on the back end". That means that they received only a minimal salary that counted against the $150 million production budget, but get a cut out of the box office take and/or the final "profit" of the film. These agreements are signed with the individuals involved Jerry Bruckheimer, Michael Bay, Ben Affleck, Randall Wallace and others and are not publicly disclosed. In addition, the film was actually made by Jerry Bruckheimer's production company (Bruckheimer Films). That company also gets a very nice chunk of the money that comes in. There are probably also lots little side deals as well in the good old Hollywood tradition of lining up at the trough.
So on the financial side there's only a limited supply of money flowing to Disney to pay off an awfully lot of expenses. But the accounting is only a small part of the story.
At the time that 'Pearl Harbor' was being put together, Disney was already slipping from its top spot in Hollywood. Eisner thought he had built Disney's reputation on mega hits like 'The Lion King'. But the follow-up animated films underperformed and the hugely profitable live action films like 'Down and Out in Beverly Hills' and 'Good Morning Vietnam' were well in the past.
When 'Titanic' came out, it dazzled Eisner. A huge, immensely profitable movie that threw Fox to the top of Hollywood (for a moment anyway). Eisner wanted one too. A single movie that would bring in gobs and gobs of cash, armloads of awards and return him to the King of Hollywood throne.
From the very moment of its inception, every element in 'Pearl Harbor' was designed solely for maximum box office potential. The 'Titanic' model was studied frame by frame. There was going to be plenty of action for the boys, a couple of young hunks for the girls, a diva spun ballad for radio play, an "epic feel" to get all kinds of Oscars when the DVD was ready, a dumbed down story for everyone to enjoy. This project had "money" written all over it. They were flat out positive this was going to be HUGE.
That led Disney executives down two dangerous paths. First, because the picture was such a surefire commercial hit all kinds of costs could be justified to "make the movie better". Example: the Hawaiian shirts worn by the two pilots during the actual attack scene. Custom designed, custom tailored, custom fabric and about $2,500 a pop. For each of the dozen so made. Made for each actor. And their doubles. And we won't even go into the flipping ship rig that has about twenty seconds of screen time. What's a few extra million when we're going to make a billion, right?
Costs ran so high that other pictures were cancelled or scaled back to feed 'Pearl'. But that was okay because 'PH' was going to be a monster hit; the Studio didn't need another hit that year even the following summer. 'Pearl Harbor' would carry everyone through quick and easy. There's no need to repeat the history of what happened to their "sure thing", but the studio cut $600 million from its already weakened production budget immediately after 'Pearl' was released. Far from turning the Studio into a cash cow, Film Entertainment became another struggling division needing a bail out from the parks.
Hollywood accounting ensures that "profit" is whatever you want it be. To the shareholders you can say one thing; to others you can say another. There is no doubt that a lot of people made money from 'Pearl Harbor', but it's not clear that it profited The Walt Disney Company one thin dime.