I have to say, I'm having the same experience. Some nights, it's fine, some nights, it's really bad. I tend to think that this is due to traffic on the Netflix side. The Apple TV may not buffer properly, and it may be the only Netflix client that doesn't degrade the stream when things slow down. But ultimately it's traffic on the Netflix side that is causing the Apple TV to rebuffer - it's just that the Apple TV isn't recognizing the need for more buffering when it does so.
One other interesting thing to support this claim: I've tried using OpenDNS and my default Verizon FiOS DNS and it seems like OpenDNS stalls much more frequently but for short periods while Verizon stalls for longer but then runs for longer after it rebuffers. I suspect that this is because OpenDNS does a better job finding servers quickly, so the Apple TV doesn't buffer as much because it thinks things are faster than they really are. Verizon FiOS DNS takes longer to find the content stream, so the Apple TV buffers more before playing. This is just a suspicion without too much to back it up.
One other lingering thought: It may be that those of us watching "unpopular" content like episodes of Veronica Mars (ahem) are more likely to experience this than people watching popular movies. Netflix's Content Delivery Network (CDN), Signal3, may be geocaching content based on use. So once the content is watched once in a geographic location, it is cached locally for better delivery. It may just be that the stuff we're watching is not located on a server near us and is therefore subject to more potential bottlenecks. This is probably not the issue but it's something that keeps gnawing at the back of my brain so I thought I'd bring it up. I would assume that all content is cached everywhere, otherwise they should get on that.
