+1 Many companies have their software available for download right on their website like the little app factory. All the user does it purchase the license directly from the site. What part of that is not profit for the software company? The Mac app store makes Apple the middle man. Why would a larger developer need Apple for advertisement?
They have to pay Paypal or whatever payment intermediary, they have to pay for bandwidth and server time, they often have complex "licencing" interactions that deter buyers, it goes on and on.