I suspect that Apple will go much farther than just allowing apps to run on Apple TV. But it will take time.
Steve Jobs famously said that the TV set-top box would need to be "torn up" and brought to market in a form that people would want to use. What I think he really meant was that Apple might be planning to tear up the entire TV industry and reconstruct it in Apple's image.
The clunky DirecTV / cable box goes away, the Apple TV circuit board (common to iPhone, iPod touch, and iPad) is built into television sets, and the concept of "channels" goes away. Tap the CNN app on your iPhone / iPod touch / iPad, and you can either stream it on that device or send it to your living room TV via AirPlay. No need to punch numbers on a remote or to navigate a menu of favorite channels or whatever. Maybe even an updated iPod nano "wrist watch" could be used as your remote.
What about DVR functionality? Not needed in Apple's future-TV world. The CNN app could allow you to watch whatever's on right now, live, or to chose any previously aired program to re-stream. No need to record it yourself with video on demand. Yup, you might have to pay a subscription fee to access archived shows. But maybe live streams would be free.
And, speaking of money, I think advertising is an integral part of Apple's plan to take over the television industry. And that means iAd. I'm convinced that iAd was designed for HDTV from the start. The first iAd I ever saw, for the Nissan Leaf, was so cinematic I immediately fast-forwarded to iAds on HDTV.
Oh well, enough fanboyishness. We'll see how far off I was in five years (or less).