updated 08:05 pm EDT, Wed June 29, 2011
Thunderbolt cable torn down by iFixit
An uncommon teardown of Apple's new Thunderbolt cable has confirmed that the $49 price comes from the quality of the components Apple needs. iFixit found that Gennum GN2033 chips are in place at each to handle the data traffic and make it an active cable, not just a passive relay. Ten additional chips are also in place for unknown purposes but which help add to the price.
Gennum's hardware is designed to guarantee "reliable" speed on copper wiring like that current Thunderbolt cables use. Future Thunderbolt cables will eventually have the option of optical cabling that doesn't carry power and might require another chip.
The components may not be completely necessary to use Thunderbolt but could make Apple's cables better than some alternatives and important to reaching its goals. Thunderbolt's support for daisy-chaining and mixing both displays as well as data may make a consistent speed important.