Ah, but it does show an effect. If you look at the same link you provided (fantastic resource there, by the way), go to the Split Statistics tab and choose career.
Under the section with the weather, there's a section showing 1st half of the season/2nd half of the season splits.
We find:
Brady 96.5/89.9 (-6.6)
P Manning 96.6/94.4 (-2.2)
E Manning 85.3/71.3 (-14)
Roethlisberger 96.1/85.7 (-10.4)
Brees 91.2/91.9 (+0.7)
Rivers 95.5/95.3 (-0.2)
Favre 88.3/87.7 (-0.6)
Romo 98.9/91.7 (-7.2)
Warner 91.0/95.8 (+4.8)
Every one of the top QBs has a lower rating in the second half of the season for their career except Brees and Warner. Where have they played? SD/NO for Brees, and StL/Arz (one year in NYG) for Warner. They haven't had to contend with the weather as often, and the numbers bear this out. Rivers and Peyton Manning also show small drops (again warm weather and a dome). Favre historically compares favorably to current QBs.
Looking a little closer, you can use that same web page and choose 3-year average. For Favre, that average is 95.5/92.0 (-3.5). He's clearly suffering a sharper fall-off from first half to last over the last 3 years running, but he's still in line with other QBs. In fact, we should expect to see less off a drop this year since he is playing home games in a dome for the first time. It doesn't hurt Minnesota also has a good defense and running game to fall back on.