From a commenter:
As a former military pilot familiar with such things, I am almost certain that Bush's flight physical did not include a drug test. (They never did with me.) You see, a flight physical is scheduled well in advance, negating any possiblity of catching someone's illigal drug usage. A drug test is always unscheduled...it has to be in order to catch a drug user off-guard. The only need for the urine speciman in a flight physical is to check for sugar in the urine and that sort of thing. Sorry, no conspiracy.
Sounds convincing to me.