In most b&m leagues, the commissioner knows all the owners, but some of the owners don't know each other. When the commissioner says, I have someone to fill this spot, and it's a close friend of theirs, nobody really puts up a fight, because it's "his league". Sometimes, that team is the commish's farm team. Other times, it's just that the commish talks to everyone on the phone or in person more often than anyone else. The best trades are often the ones where two owners are talking to each other off and on for a few weeks and finally decide to make a move. That doesn't happen if you're not talking off and on for a few weeks.
Also, the guy with the most interest in starting a new league or keeping a league together over the years is a good player. Someone who has never played before isn't likely to organize a league at work. Someone who struggles year after year isn't likely to volunteer to commish the league to keep the thing together. It's kind of like that one guy you know who owns his own poker table/paintball equipment/bowling ball/pool table/whatever - if you're good at it, you're probably going to try to get your friends to do it. So naturally the commish is going to be one of the better players in b&m leagues.
On the other hand, in leagues where everyone is active and knows each other, or online leagues of relative strangers, the commish really doesn't have much of an advantage.