I want to believe NOP is clean but until they are much more transparent there is going to be tremendous doubt. That's why athletes like Galen have to be open and transparent, not because they themselves have crossed the line but to prove to the public that they are clean. Sad reality of having to overcome what past generations have done to our sport.
I am not suspicious of Rupp per se but rather the people with whom he associates. Salazar, Knight, Stray-Gundersen, etc. do not have the best reputations.
Watch the dynamics of the Rupp-Salazar relationship in the BU weight room. Do you really think Rupp would question Salazar if the latter instructed "Take these multivitamins?"
If Rupp was running for a different company I wouldn't doubt his performances for an instant. The same reason I don't doubt Hall, Simpson, Huddle, and the like.
It is naive to assume one is clean simply because one hasn't failed a drug test. How many did Armstrong fail?
I truly hope all Nike runners are clean but it is nothing we can just blindly assume. These kind of questions do need to be asked. Public TUEs are a great idea.