NFL Football for sure is a different animal. I see what you are getting at. I think the big reason why it doesn't seem like the best football team from each conference doesn't get in is because of the Salary Cap. Now there isn't much difference between an 13-3 and a 10-6 one. Plus like others have said it's one and done. If the QB has a bad game that's it.
In baseball only reason upsets happen is because a better or pitcher can get hot and carry a team to a series win.