Andrew Sullivan asks if there is an argument with "a modicum of sense" for banning marijuana but not alcohol. The argument is simple: alcohol is regrettably too culturally pervasive for a ban on it to be politically sustainable, while marijuana, fortunately, has not yet achieved that status.
I find it useful in these discussions to define a concept which I'll call, for want of a better word, "vice". A vice is an activity with two properties: (1) a great many people enjoy indulging in it, and (2) some non-negligible fraction of those people (call them "abusers", and their relative numbers the "abuse rate") cannot do so without seriously harming themselves and/or those around them. All the illegal recreational drugs are vices, as are, for example, guns, gambling and perhaps even fast driving. (I prefer to exclude tobacco and fatty food, since limiting a lifetime to the low end of the natural span strikes me as far less catastrophic than destroying the life of an otherwise healthy, productive adult, who may be a provider for a spouse and small children. And other drugs, such as caffeine, simply don't cause enough damage to be called vices.)
Now, I generally support social suppression (including even criminalization) of vices, on the principle that pleasure and joy are relatively easy to obtain without jeopardizing self or society, whereas safety is much harder to come by, and thus deserves greater societal effort and sacrifice. On the other hand, I recognize that there is a legitimate libertarian argument for treating vices as risks that each individual should be free to accept, along with their possible consequences. One could even imagine a finely-tuned intermediate position that weighs the social cost of a particular vice against the "philosophical cost" of restricting it.
In practice, however, the body politic adopts a far cruder approach: voters invariably defend their own freedom to indulge in vices they (or their preferred social circles) happen to enjoy, while advocating bans on vices they personally abhor (or from whose negative consequences they have directly or indirectly suffered). For a good example of this phenomenon, try watching a typical Democrat and a typical Republican debate drug laws and gun laws; they will inevitably swap not only positions, but also arguments--sometimes practically word for word--as the debate shifts from a fashionable Democratic vice (recreational drugs) to a favored Republican one (guns) and back again.
As a consequence of this political reality, vices with a sufficiently low abuse rate (such as alcohol) become politically invulnerable once they achieve a high enough level of popular use. That doesn't mean that they don't devastate millions of lives; it merely means that the constituency of happy non-abusers will handily outvote the victims every time. Marijuana has not reached this threshold yet; but if it is legalized, it may well one day achieve the status of a second alcohol, in terms of both destructiveness (number of ruined addicts, disrupted families, marijuana-related accidents, and so on) and political unassailability. I have no desire to hasten the arrival of that day.