Two reasons, the digital output is better than the output on the AEX which is jitter prone and will not lock to some external dacs and in it is a more spphisticated device running a version of iOS8. It is expected that the ATV will have native support for the Apple/Beats streaming service expected on the next few months.
Of course if yo have no plans to use an external dac or use the streaming service, it matters not. Which really brings us to the point, there are hundreds of ways you can stream from your iThing and depending on what your priorities are, some methods will be better than others.
In this case you have gone for a fairly purist hi-fi approach, stripped down amplifier fed by the AEX and good small speakers. You are therefore totally commited to Airplay which is fine as far as it goes, if that is all you need and want then that setup will be excellent.
You may wish to do other things though, access streaming solutions, set up your own music library or upgrade in terms of sound quality other solutions may be more flexible.
For an ultra high performance in an even more stripped down package you can run the AEX directly into high performance active speakers, Yamahas HS8s have fantastic room filling capability for their £400 price tag, whilst the smaller Equator D5 offer outstanding perfoemance for relatively near field use, both outstanding performers.
At the other end of the scale, the Yamaha Rn500 offers all the functionality you might need, built in dac, Airplay, network streaming, Spotify Connect, digital radio and the rest, still within budget too.
As I said it really depends on what you think your requirements and priorities are, it is all up to you.