Projectiles IMO don't really hurt any one character more than another, except in cases where the character in question is very slow. The answers most characters have for fighting projectiles are universal.
Most approaches in Brawl are mix-ups anyway. Very few characters have approach options so profound that they can simple barrel or even PS/shield through a projectile wall and attack with X and win every time. It's just a fact that at long range, projectile characters have the advantage in that you are approaching them, or reacting to them, even if said projectile game isn't very good. This goes for everyone from Samus to Peach to Toon Link to Falco.
With that said, I'm not convinced Falcon is terribly hurt by projectile games. If anything he's better-equipped to handle it than most characters given his fast ground speed and good air speed, and above average aerials. It isn't like he has the Ganon/Zelda problem where he moves so slowly that he can't cover any ground between defensive maneuvers. =/
In addition, I believe that time will show that we have dramatically underrated Captain Falcon. His biggest problems are fall speed/weight class-related problems like chains and combos, and a "bad approach game" which I addressed previously. He also sometimes has problems scoring kills because his kill moves are all strong punish moves and aren't super-reliable. His strong jab and good mix-up game combined with his better-than-average recovery and "burst of speed" game (in which he can quickly change course and do something unexpected much like ZSS, Sonic, Fox, and Wario) are all very good qualities. We just need a very talented player to step out of low tier games and show us how wrong we are. No, I'm not arguing for a rise for Falcon.
