Well there certainly is alternatives for Linux that are perfectly capable of encoding and playing back HD content. After all it's perfectly possible to do HD video production work in Linux, and people do.
However the blame isn't linux. It's Apple and their codecs. If Apple felt like letting Linux users use their codecs and such it wouldn't take any more then a tiny bit of effort on their part to make it work, but they don't want you to be able to do that. They want you to buy a Apple or use their software in Windows. (it's a control thing)
Just like they don't want to let you to use content bought at Itunes work in Linux, or use Ipods in Linux. (but people do anyways, they just hack around the problems)
Also keep in mind that Quicktime isn't so much a video or audio format, it's a container file. You can have different types of video and audio content in a quicktime file. So probably what is happenning is the first part of the quicktime file has video and audio encoding that can be played back using VLC and such, but the second part is encoded using something else.
Maybe that H264 thing barnett26 was talking about.
Check out Ubuntu's website. There are guides on doing the easy way to install support for restricted codecs and files and such. By following those guides you can get 90% of everything to work just fine in Linux. However there still is some stuff that people haven't figured out work arounds for the restrictions that companies like MS or Apple put on their stuff.
So there is still a decent chance you can get it to work fine, but don't hold your breath.
