One of the producers of the game addressed Brady's THP rating about a month ago:
http://www.easports.com/madden09/fullsite/blog.jsp
How Do I Rate Him? Tom Brady and 99 Throw Power
A lot of people started questioning mine and EA's sanity when Tom Brady showed up with the strongest arm in the game. A false belief that a lot of football fans carry when judging quarterbacks arm strength is that their arm strength stays the same from when they enter the NFL from college. If my D-League softball arm has gotten stronger from half assing it at a gym 1-3 times a week then imagine what a determined guy working with an NFL strength coach can do. It is obvious that Tom Bradys arm has gotten stronger since he entered the league. Another example is Drew Brees. He was known for having a weak arm out of college and didn't show much in San Diego to change that perception. But after his shoulder surgery rehab and going to New Orleans his arm was clearly stronger and he threw the ball deep more than any quarterback two seasons ago. He does not have the velocity that other quarterbacks have but can stretch the field with his arm strength when he has receivers that can stretch the field and did so many times during the 2006 season. JaMarcus Russell last year had the strongest arm in Madden last year at 99 Throw Power but Tom Brady consistently proved week after week during the season that his arm was the best as he frequently threw the ball 50+ yards. From what I hear Russell's arm is at the top, but it is something of a legend, as he has yet to prove it in an NFL game. And it's tough to get too pumped about these stories about how he can throw the ball 50 yards standing on his head, because I remember hearing something similar about Kyle Boller and I have yet to see him throw from his knee on Sunday. In addition the two former college quarterbacks that work at EA both believe Brady's arm is the strongest in the league. And there is nothing to think that he won't keep airing it out with Randy Moss back while Russell does not have a big time deep threat in Oakland. That being said if JaMarcus comes out there and starts breaking hands with fastballs, then he will get his due.
There are 2 examples that stick out in my mind as to why Tom Brady has the strongest arm in the NFL in addition to the Dolphins game.
Jets Game - This was an eye opening throw for me way back in week 1, this is where the 99 THP rating was born. I actually was laughing at high this throw was across the field 65 or so yards.
http://www.youtube.com/watch?v=vfAEoz75a2k
Super Bowl - Some people might have brushed this aside because it was just a long incompletion the second to last play of the Super Bowl. The TV broadcast showed the ball a little better but the ball is on a line about 15-20 yards off the ground, across the field, around 70 yards in the air. There is no other QB in the league that can make this throw.
http://www.youtube.com/watch?v=YwyGW5j64DU