First, a disclaimer: I am no Floyd apologist and I make no excuses for him. I've actually been pretty outspoken in the past regarding everything that went down. Also, while the topic is omerta and there is pressure to follow the silent rule, there is ALWAYS a choice. It's a mafia term, but cycling isn't the mafia.
Having said that, here is my take.
Regardless of the Monday morning quarterbacking, and the clarity of hindsight, when Floyd got popped, he found himself in a position never before encountered in the history of professional cycling. He got popped WHILE wearing the leader's jersey in, and subsequently winning, a Grand Tour. Not just any GT, but the Tour de France. That had never happened before. Never before, even in the Cofidis scandal or others before that, had the doping spotlight been shown directly and brightly on the maillot jeune.
There was no script to follow, no prior example to look to, and no simple solution to the problem. Plus, even though he had been riding in the European peloton for several years, he was still something of an outsider. Armstrong had just won seven Tours in a row, and now along comes another American, except this one has very few palmares on his resume, beyond being a super domestique for LA. Floyd didn't enjoy the popularity or authority of his predesessor. Let's face it, there are riders who are deemed worthy to win, who have the "right" to win, and then there's everyone else.
Instead of the typical brushing off of a positive (either through a payoff or other means), Landis had to go into super-omerta mode, likely at the behest (or demand) of several in the heirarchy of the peloton. He was likely told to do what he had to to make sure the yellow jersey didn't have a doping stain on it. Floyd was told to clean up his mess, at whatever cost. It was never about Floyd's best interest, but the desire to maintain the status quo.
It's really not hard to imagine just how many people would like to see that stain erased. Riders, sponsors, teams, even the organizers would be best served with a fight to clear Landis (and in turn the jersey and the Tour) rather than a record book with a doper stripped of the jersey. Capitulate or go down fighting in the hope that a test goes bad or some technical error is committed. It seems like a pretty easy choice (not for Floyd, but for those calling the shots), especially when so many powerful people have so much riding on keeping the image of the Tour untainted. It's kinda like the need for finding WMD's in Iraq shifting from de-arming a dictator to justifying an invasion. Same play, different goal.
Add to all this, the very real likelihood of a complete blacklist and loss of any hope of racing professionally again, and the picture becomes complete. Floyd does whatever he needs to do to clear his (and the maillot jeune's) name, except he still gets blacklisted and left for dead by the very people he fought so hard to satisfy.
Again, just my take. YMMV