I also think part of this is due to the BCA allowing pretty much anybody to run a BCA sanctioned league. Whereas with the APA, it's a franchise deal - and those franchisees pay money for exclusive rights to their area.
That said, the APA LOs generally have many more players in their leagues than your average BCA league-running guy, which means lots more work, which often means it's work on the level of a full-time job, which means they have to make a living somehow. Most BCA league operators, as best I can tell (and correct me if I'm wrong) run one, maybe two divisions, one/two nights a week, often in the same room (i.e. low travel costs), and spend a tiny fraction of the time handling their leagues than their larger APA counterparts.
Plus, in my limited BCA experience, the BCA leagues cost more ($10/week vs. my old APA league which was $5/week). I'm sure league costs for both types vary regionally.
That said, I figure it's easier for one guy running one league night a week, collecting more cash per week per player, to give more back at the end of the session than it is for your average APA LO.