They are based on a statistical formula (DVOA, see footballoutsiders.com), and its a classic example of stat geeks taking something that works fine in baseball and assuming it'll work in football, and being utterly wrong. This week the dolphins dropped in the rankings due to the way they are weighting results over time (and in a fashion that would make my old college stats prof scream in horror).
Baseball is a very controlled environment consisting of a single repeated event with only a few changeable factors. Hence stat geeks can go crazy and come up with some very meaningful statistical analysis. Football meanwhile has many variables in place on every single snap, overall results decided more often by big plays then steady statistics, and a sample size of just 16 games instead of 162. So as a result its a case of lies, damn lies, and statistics.
So whenever a football article starts with "according to stats gathered by", click back on the browser.