Actually I very much doubt apple have a good reason for leaving the optical out, I suspect it was a decision made but some mid level manager probably supported buy some flash presentation and the real potential impact was not picked up by senior manager on sign off. Happens all the time in big company's , even apple these days unfortunately
I honestly think that, this being Apple with their tendency to drop "old" standards. Has just decided that at this point in time, with A/V receivers having included HDMI for so long and the Apple TV being pushed as a device for the TV. That they don't need optical anymore, that the majority of the market will be just fine with only HDMI. They're probably right as well. Apple spend an incredible amount of money on market research to make sure that they are making the right choices overall.
There's always going to be a subset of people at these transitional stages that aren't happy with the choice. But let's face it, HiFi purists (disclaimer, I'm an Arcam guy
) have options to expand without replacing everything.
Most quality HiFi equipment doesn't have optical as standard anyway, we need to buy a seperate DAC for that and even those are starting to include HDMI in some cases. Off the top of my head the NAD M51, Essence HDACC, to name a couple.
That's before we get into the various breakout boxes ranging from the cheap, to the ridiculously expensive.
The issue, really is that some people want something Apple has decided has become irrelevant to them. Is it fair, or the best choice to have dropped optical? Possibly not. But nor is its Apples responsibility or duty to cater to that particular market either. They've positioned the new Apple TV as a device for the television, oddly enough, and chances are that a large portion of purchasers will be hooking it up directly to a television.
The next biggest demographic will probably have A/V receivers or sound bars that support HDMI. That just leaves, what to Apple, is probably a fringe market of people who want optical.
You'll find plenty of people willing to shout and complain about the situation, but compared to the millions you don't hear complaining because they just don't care, or notice that it's not there, not such an issue.
I'd have liked an optical out on the new Apple TV. Do I care it's gone, not really, just more fuel for the fire when I decide to convince the wife I need a new amp