It,s just one of the many athletes that got caught for doping and has been able to elude it for a decade because his doctors and his techniques were ahead of the time. It,s like the Balco scandals, if it wasn't from an inside source, many athletes would have eluded tests; better doctors, new techniques...
There is way too many witnesses on that one and the samplers have been tested and re-tested and the labs who did perform it (including Chateau Malabry in France) are among the top labs in the world. Is he guilty? To me, 100%.

HOwever: the tour de France is notariously famous for being filled with enhancers users, back in the 60' the Pelissier brothers (Henri and Charles) were showing to reporters the pills and other stuff that they were handed by the tour managers in order to complete. At the time, the idea of cheating by taking enhancers wasn't spread neither much acknowledged.
In the meantime, these produces got prohibited and some tests (severe?) got imposed to find the cheaters but the cheating culture was already well rooted.

Though Amstrong deserves to lose his titles, what's sad is that he's just one of all those who did cheat, I am about certain that around 50% of the runners have some skeltons in their closet at some point and because he did win a lot, he's the one singled out for it.