The other answers mostly sum it up - it was initially made illegal primarily as a way to establish an "other" with which to frighten conservatives.

There's another thing that hasn't been mentioned yet though that I've long thought is relevant - is part of the reason that marijuana specifically was for so long (and still is in some quarters) so condemned.

Imagine you're a corrupt politician, and you want to sell your constituents on the idea of going to war in the Middle East (so you can collect some bribes from defense contractors and oil companies) or instituting mandatory sentencing (so you can collect some bribes from prison contractors) or cutting taxes on the wealthy (so you can collect bribes from rich people and corporations) or any of the other, similar things that corrupt politicians want to do

Who would you rather try selling that idea to? A bunch of pot smokers or a bunch of drinkers?

I think part of the issue is that marijuana appeals to a part of the population that really is, to corrupt politicians and their cronies and patrons, "undesirable." When they want to get the people all fired up in support of their latest bullshit, they want somebody with a beer in their hand, drunkenly shouting, "Yeah! Kick their asses!" Not somebody with a joint in their hand, muzzily saying, "Hold on a minute - you want to do what?"