Right now Linux support for Thunderbolt technology isn't critical considering the lack of systems offering such ports and there not being many peripheral devices to actually take advantage of this technology compared to USB 3.0, eSATA, or Firewire. Fortunately, it's being worked on and should be properly supported by the time more systems begin offering these ports that are pinned out the same as mini DisplayPort. Bringing up the support isn't a huge feat considering Thunderbolt is effectively just pairing together PCI Express and DisplayPort, both standards already supported in Linux. Thunderbolt will make its way to motherboards, graphics cards, and add-on cards.
Intel developers from the LAN Access Division are working on the Linux support for Thunderbolt. In particular, "LAD will be supplying initial software for peer-to-peer use in Linux and other OSes. LAD will also be working on enablement code for Open Source OSes so that others will be able to use that code. LAD may also supply other use case but initially only peer-to-peer will be done." This comes from a presentation to be made next month at the 2011 Linux Plumbers conference.
Look for more information to be reported on Intel Thunderbolt / Light Peak Linux support during this conference taking place from the 7th to 9th of September in Santa Clara, California.