Landis is being punished for daring to defy the anti-doping authorities, insist on his rights to a public hearing (no longer allowed), and embarrassing the hell out of the USADA and WADA by absolutely demolishing their scientific credibility with regard to the testosterone case (after they had to dig in their heels because they had already illegally released the preliminary reports, pre-B sample test to the media). I would note that in the original (and appealed) decisions, the panels through out the initial T-E ratio test as being hopelessly compromised. The mass spectrometry tests were allowed to stand, despite being the quality of lab work that would get laughed out of a college chemistry class, because both panels chose to totally disregard the testimony of John Amory. (see: http://rant-your-head-off.com/WordPress/?p=383 or http://trustbut.blogspot.com/2008/12/winnowing-john-amory.html)
Now, as it turned out, Landis later admitted to doping with HGH that season, and testosterone in previous seasons. But I really think that's incidental to this case. He's being punished because he showed the WADA and UCI are just as corrupt as the cyclists, and the Chatenay-Malabry lab technicians are too incompetent to run a mass spectrometer that undergraduates successfully use thousands of times a day in research labs.