It is important to remember that the ATV upsamples/downsamples everything to 48khz. This resampling can have a very profound effect depending on your equipment. That said, I have tried numerous other 'bit-perfect' media players against my CD player and often find that they do sound different. I can only attribute the difference to the transport mechanism within the CD player as being the variable.
The Cave: Sony VPL-VW600ES, 110" Elite Fixed, Oppo BDP-103D, Apple TV 3, Emotiva XMC-1, 3 x Emotiva XPA-1 Gen2 , 4 x Emotiva XPA-1L, Sonus Faber Venere 2.5, Sonus Faber Venere Center, 4 x Emotiva ERD-1, 2 x Rythmik FV15HP