I've asked a similar question before, and I know that part of Columbia's problem (I think) with profits was that they didn't own any studios. However, it was mentioned in an article that "You Nazty Spy!" was budgeted at $18,000. Of course, this was back in their heyday, so obviously there'd be a good-sized profit. But even if we look at a short such as "Flying Saucer Daffy", I'm going to assume that the budgets for the shorts did NOT go up, (I believe both Moe, Larry, and Jules White mentioned this) so if it was budgeted at, say, $20,000, how could Columbia NOT make money? I know that the shorts weren't released to every theatre in the country (and overseas), but I find it hard to believe that losing money was the reason why the Stooges were let go in 1958. Now, if they'd said that the audiences were changing, double features were on the rise, and there just wasn't any place for the shorts, I could believe that. But unable to make money? It shouldn't have been that difficult to make a profit on a $20,000 film, which may have been even cheaper due to the cutting back of the shooting schedule and use of stock footage.
I'll admit--I know nothing about the business side of movie making, but I always found this a little fishy.