using my ratings, produces the following QB ratings thru the first 4 games

(for ref, see http://www.nfl.com/stats/categorystats?tabSeq=1&statisticPositionCategory=QUARTERBACK&season=2009&seasonType=REG)

QB               Rating rank (mine)     NFL rank               TG          TI          YG          %compl

PManning  (IND)          1                    1                    2.25          6          334          70.8

Favre   (MINN)               2                        3                    2          9          209               69.1

Brees  (NO)                 3                    2     

Flacco   (BAL)               4                    10                    2               5          276          62.9

EManning                        5               4

Schaub  (HOU)                 5                    7

Rivers (SD)                6                    12                    1.5           3          311          58.7

Roethlisberger               7                    8

Rodgers  (GB)                8                         5

Let's examine some of the more diverse (Rivers,Flacco vs Favre,PManning)

Essentially the NFL rating is penalizing Rivers and Flacco for a reduced % completion.  Favre's lower yardage production is not penalized.

IND and SD differ by only 5 total offensive points, though Manning's %compl is 71 vs Rivers' 59

I would ask what leads to scores, yardage or %completion?  Yards bring scoring position and thus points

The shame is Rivers is a top 5 rated QB, while the NFL doesn't  place him in the top 3rd of quarterbacks (12th out of 32)

Let's look at offensive points for the QB's teams with 100+ points thru the 1st 4 games:

                         QB yards/game          %completion(RND)

NO 144                    258                          67

BAL   124               276                             63          

MINN  118          209                               68

NYG 107               260                             63

IND  106                334                            71         

CHI  105               225                             64        

GB  104               275                              61

SF  102               175  (outlier)                  62

SD  101               311                           59   

Now, if we order the QBs by highest %completion, the associated teams in order are

PITT,IND,MIA,MIN,NO,SEA,ATL,ARZ,WASH,PHI  which contains only 3 of the top scoring teams above

Using my rating, the 0-1 ratings for various QBs is:

Brees 0.500     (0.20*(27+2)/11+0.20*(27-9)/100+0.20*0.681+0.20*(3000+28)/11/100)/2.5  (11 games)approx

Rodgers 0.494  (0.20*(22+3)/11+0.20*(22-5)/100+0.20*0.655+0.20*(3136+247)/11/100)/2.5  (11 games)

PManning 0.489 (0.20*(24+0)/11+0.20*(24-11)/100+0.20*0.698+0.20*(3415-3)/11/100)/2.5  (11 games)

Brady 0.480     (0.20*(20+1)/10+0.20*(20-6)/100+0.20*0.664+0.20*(3049+43)/10/100)/2.5  (10 games)

Schaub 0.447  (0.20*(21+0)/11+0.20*(21-11)/100+0.20*0.678+0.20*(3142+51)/11/100)/2.5   (11 games)

Favre 0.451      (0.20*(24+0)/11+0.20*(24-3)/100+0.20*0.680+0.20*(2829-2)/11/100)/2.5   (11 games)

Rivers 0.424  (0.20*(19+1)/11+0.20*(19-6)/100+0.20*0.642+0.20*(2938+46)/11/100)/2.5  (11 games)

Roethlisberger 0.424  (0.20*(14+2)/9+0.20*(14-8)/100+0.20*0.679+0.20*(2469+38)/9/100)/2.5  (9 games)

Flacco 0.385  (0.20*(12+0)/8+0.20*(12-7)/100+0.20*0.649+0.20*(2044+45)/8/100)/2.5  (8 games)

EManning   0.370   (0.20*(13+0)/8+0.20*(13-8)/100+0.20*0.579+0.20*(1855+40)/8/100)/2.5  (8 games)

Soon you can play with my javascript form for the rating HERE (NOT YET!!! has bug): JAVASC~1.HTML  (note: the shown Montana xample is incorrect)