Because you can't launch an auto properly and must start moving between 2000rpms to 3000rpms (if you do a brake-stand) or from idle, if you just floor it. With breather mods, such as the CAI
, you lose a lot of valuable low-end power. You need low-end on an auto if you want to move. With that lost, your car will move even slower off the line then stock, and you won't see any improvement until past 5000rpm. So that is why they say breather mods are bad for the autos (on our cars specifically & all other low-torque motors in general), because you lose power where you need it the most, which is down-low.
For manual car, losing down low doesn't really matter much, because you can launch above it, and after that its all high rpms.