First point - depending upon the film and the distribution deal, MOST theaters do NOT keep a "hefty percentage." They make their money on concession-stand carbs and sweets. There are some distribution deals that leave the theaters mere crumbs as their "percentage." We don't know the details of Mel's deal with the exhibitors.
You're certainly right on the second part, though. Release prints are comically expensive and have a finite run before the optical quality of the print deteriorates. They're also heavy as lead to ship, which is more $$. And Mel has hired an ad agency to buy tons of network TV air time, which isn't cheap. Of course, the schedule they bought was probably only a two-week flight, but still...
My take is that the film will be firmly in the black before it hits the retail DVD/Video market, and that it will REALLY take off when that release hits.
Fortunately, Mel isn't using the "Usual-Suspects Accounting Methods" developed by Hollywood over the years, designed to shield all but the wildest profits from investors or to turn even the biggest hit movie into a paper loss for tax purposes. No, this movie will be accounted for fairly.
Michael