I think the way it ultimately works is that you have to be disillusioned from the grade-school fairy tales told to the public about how science works before you can learn to live and work in the environment that actually exists rather than the one you wish existed.
> "Never question a scientific superior?" Not parsing that concept, please elaborate.
tech < grad student < postdoc < junior faculty < full prof < Big Guy/Gal < Nobel Laureate < NIH Director
People above you in that chain will accept limited feedback on methods to attain their chosen goals and will greatly resent questions about whether their selected goals are worthwhile/realistic/rational, or whether their gestalt vision of the field's conventional wisdom is correct.