If you play it through a different DAC, sure. But that's not a failing of the CODEC, which is the picture you're trying to paint. Rip a CD to Apple Lossless, re-burn it to Audio CD, and play it in the same CD player, and you'll not hear a whit of difference. What's more, if you play an Apple Lossless file through the Apple TV's digital output over HDMI or S/PDIF into your receiver, you won't be able to tell the difference because it's going straight digital (the same as a CD's output) into your receiver's DAC.
Fair enough. But if I take my iPod and connect it to my processor/receiver there is a difference and also connecting my iPod to my car stereo and playing the CD in the car stereo. What I gain with my iPod is convenience and portability. I don't have an Apple TV yet and will get one when iTunes supports DVD-Audio and SACD.
What the original article is saying or asking, is for a better high-res CODEC to be developed where people would pay more for the music. Is this unreasonable since many people already have good music systems in their homes with home theater?