I think people try to regulate morality (cause really thats what prohibition is) because the stoner getting stoned and then having the audacity not to die is an act that flies in the face of the moral beliefs of the establishment.
Also one needs to realise that the basic morality of the establishment is one of a sort of base-line christianity, and that type of morality implies that those who believe are duty bound by their belief to try and convert others to their way of thinking.
When someone follows a different path, one that the established morality says is destructive, and yet said someone not only doesn't fail at life, but accels that is seen as almost an insult to the morality that denounced the destructive path so the follower of that path must be stopped.

Note that I am speaking in some broad generalizations. I do realise that some people out there have no intention of forcing their morality on others.
This is just an attemp to explain the type of general mindset that leads to things like prohibition.

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Still today, you can go up on a steep hill in Las Vegas and look west, and with the right kind of eyes you can just make out the high water mark, that place where the wave finally broke, and rolled back.

- Hunter S. Tompson