Engine braking allows you to save fuel (by using stored energy of the drivetrain to handle compression of the air that normally would require work from combustion).
And, as long as the car remains in gear there's not much extra wear on the transmission itself (certainly not compared to the torque from the acceleration the preceded it, at least).
I think we're talking about different things. digitalWestie's advice to use the gears to slow implied changing down through the gears to use the engine to brake, not simply leaving the car in gear while applying the brakes.
For what it's worth, it does makes complete sense to leave the car in gear while braking and not to change to neutral.
And, as long as the car remains in gear there's not much extra wear on the transmission itself (certainly not compared to the torque from the acceleration the preceded it, at least).