I believe the Lance Armstrong affair does not reflect on Nike, surely it beggars belief a huge corporation like Nike, with their intimate knowledge and involvement in sport had no idea what was going on with Lance Armstrong. It seems to me Nike were happy to be associated with Lance Armstrong and make lots of money on the back of that association, and turn a “blind eye” to the rumours until Lance Armstrong became too much of a liability.
If you take an overview, not only does Lance Armstrong come back from cancer, but (according to him) beats many riders who have now admitted doping, cleanly, incredible! Also the present generation of riders (Wiggins, Froome and co) are performing about 5% less (in terms of power) than Armstrong´s era. 5% is about the advantage successful doping will give you!