There have been a number of articles about the Apple TV and it's "one missing feature", the television tuner. As much as I can see why people would be interested in having a DVR on it, I think Apple chose wisely in not putting one (or more) into the box. I'll go through the reasons here.
First, 40GB is great for a device on your bookshelf or next to your TV, but it's really not enough for your DVR. I have one with a 250GB for pulling in HD content and that's just not enough if we're taping all HD. Having removable, replaceable hard drives is costly, as is having multiple versions of a device that is very comfortably priced at $299.
Next, there are many too many standards and sources out there for a single tuner to do everything. Yes, I know... CableCard, but that's not sufficient for my needs, because DirecTV doesn't support it. They could put in something to do manipulation of a dumb tuner, or various other things, but that's going to be a lot of debugging, and Apple (and more importantly Steve) really couldn't deal with a solution that is as kludgy as having two devices talking to each other over IR without any handshaking. It's too prone to error, best to leave the recording problem to somebody else.
Besides, the eyeTV from elgato and products from others do a good job of getting the media to your Macintosh, iTunes does a good job of managing it, why not just allow the Apple TV to keep what you need immediately on it? Especially since iTunes can sync your 10 most recent unwatched items... that seems very likely to be a great use for this.
Also, it certainly looks like a good opportunity to use Roxio's Toast 8 software to grab your shows recorded by your TiVo and plop them on your AppleTV.
In the end, I think people will miss the tight integration, but the home theater market isn't up to that yet... unfortunately... and they aren't moving in that direction either.