I think how many teams are in your league makes a big difference when answering this question.
If 10 or less - I don't think it was a very good idea. Scarcity at QB will not be enough for someone to trade enough value for Brady most likely. I would also asume your depth took a hit due to the grab.
12 team - I'd say this is debatable. I personally don't have a problem with it especially if it is 6 points per pass TD. In that case I think you grabbed good value in Brady who fell too far and could pretty easily flip him for what your team needs down the road. I also am not against drafting Brees or Rodgers in the later first round. You just have to be confident that some of your picks later in the draft will hit. I personally like to load up on RB's late if I am taking the QB early.
If 14 teams or more - I believe it was a very good move. I'm sure you could get nice value from either, value that would be worth more than a 6th round pick.
1st $12 Team Return 2 Flex 6 TD pass Keeper -Yahoo Sunday Black n' Blue
1st $12 Team Return 2 Flex -Yahoo GRIDIRON MASTERS
1st $12 Team PPR 2 QB -Yahoo MeanAssStaleys
3rd $12 Team Return 3 Flex No Kicker -Yahoo Td's N Beer