This is going to sound anti-Apple, but if you look at how Apple conducts business, it makes sense. They thrive on a consistent user experience which means an Apple TV could guarantee the same refresh rates, resolutions, features, and perhaps even screen sizes. That's not to mention guaranteeing there's a webcam on each and every TV (something you can't guarantee with a box, since it would require the consumer hook it up and place it above/below the TV (same with any kindof motion controller thing).
They also love to lock people into iTunes or other Apple services. By having a dedicated TV, they can effectively lock out other devices or applications (Netflix doesn't pay them to have an app, then AppleTV owners don't get access to Netflix....they could in theory even set it up that it would recognize a Roku box was attached and lock it out).
Also, look at how they have handled in-app purchasing (Apple gets a whopping 30% of any in-app purchases). Picture being able to order a Vudu movie on the Apple TV app for $6.99 for example, and Apple would most likely be taking a 30% cut of it (or over $2) because they're allowing Vudu the privilege of selling us something through an app.
Yes, they could do the same thing with a standalone box, but with it being tied to the TV, they may (as mentioned) be able to recognize that you hooked up a Vudu box and lock it out. I'm not sure they would because of the potential outcry, but it's certainly possible.
The point is, they try really hard to lock you into the Apple/iTunes ecosystem with their products.
Plus they can charge twice as much for having an Apple Logo then release the same TV later that year in white to keep in the news