Why do you think Jeff Atwood's reputation points on meta has reached 7,733 in just 37 days, while on Stack Overflow it's only 14,371 after a year?
On Stack Overflow, he is just a well-known user of above-average skills.
To paraphrase The Matrix Revolutions:
Down here, he's god.
Basically, he runs the site, and I'd say a lot of people +rep him by default when he posts.
He's the authority on MSO. Every answer he gives is the answer.
I heard he has root on the box and will fiddle with the database sometimes.
Obviously, he's more active on this site than SO.
It may also be the nature of MetaSO... Rep seems to be more easy to come by here. Hell, I'm earning Rep twice as fast here as I am on SO.
Probably a large part of it is due to the fact that he responds to feature-requests and bugs as the creator of the system - i.e. the guru / authority on it all. It is a bit hard to argue with him when he says that e.g. voting does work the way it has been designed to work, etc. Obviously, there are some things that people will disagree with and down vote him on, but since the up-votes are worth so much more, he will likely come out ahead in the end.
If Jeff didn't delete all the Meta discussion on SO after the private beta, he would probably be number two behind Jon Skeet on SO.
It is funny, though. If you look at his rep, there are a lot of down votes. I guess some people have issues with authority.