The reasons are philosophical and cultural, political, geo-political, and economic. First the philosophical and cultural, the western mind likes order, it objects to people staring into space and giggling. More to the point it objects to free thinking whether pot induced or the rebellion it symbolizes against authority. The idea of a mind not tethered to production for the capitalist economy, obedience to the corporate managed state or the superstition of the church is repulsive to the managers of these institutions.
The cultivation, processing and enjoyment of marijuana is free from government interference and control, it is a threat to every form of control. Unlike alcohol, tobacco, methamphetamine, heroine or cocaine, it doesn't require any fancy processing; grow it, dry it, smoke it. In fact grow it in your closet, as a lot of folks seem to be doing, half of all domestic production is considered to happen indoors in the U.S. After that you can improve on your methods.
But the reality is anyone can do it. It is totally democratic, accessible to anyone no matter what their income status, which is a threat to the system. It is a valued commodity that corporate capital can't corner the market on, the government can't regulate and the church can't match the high. It is a source of income to those who refuse to be slaves to the wage slavery of modern corporate capitalism. Because of those reasons the government hates it, capital hates it and the church hates it.
I cannot emphasize this enough; the sheer democracy of having free access to a non-harmful herb that alters your mind in a pleasant way threatens the ability of these institutions to make you feel powerless in their shadow. It is also natural for so many people precisely because it caters to their indigenous roots. Everyone has a natural desire to get high, little kids spin in circles until they fall down from dizziness. Before spreading to the west the use of cannabis in central and south Asia can be traced to the 3rd millennium BC. Use was widespread and practiced in China, India (the term ganja is Indian), Nepal, Bulgaria, Greece, Turkey, ancient Assyria and Sufi's in the Muslim world.
Marijuana was only regulated by countries at the beginning of the 20th Century and it wasn't until 1937 with the Marijuana Transfer Tax that a real ban came about in the U.S.
That was primarily based on a public relations war by Harry J. Anslinger the head of the Federal Bureau of Narcotics and reports from the agency that they were seeing more people smoke marijuana.
Anslinger is credited with such words of wisdom on marijuana as: "There are 100,000 total marijuana smokers in the US, and most are Negroes, Hispanics, Filipinos, and entertainers. Their Satanic music, jazz and swing, result from marijuana use. This marijuana causes white women to seek sexual relations with Negroes, entertainers and any others." And such gems as: "Reefer makes darkies think they're as good as white men." and "Marijuana leads to pacifism and communist brainwashing." No proof of any further deleterious effects was necessary for passage.