I think I'm being inconsistent. I'd be inclined to agree with both of the following statements:
(1) Most recreational drugs should be made legal. Not just relatively safe drugs like marijuana but also some of the nastier stuff. I'm not sure how far I take this: the relative ease of addiction and debilitating nature of withdrawal symptoms might make a drug like heroin bad enough to warrant legal proscription, though not with the severity of current laws.
(2) The distinction between prescription and non-prescription medications serves an important purpose and should be maintained (without saying that everything is on the side of the line where it should be).
The inconsistency isn't as wide-spread or obvious as it might seem. Many legal prescription drugs are much more dangerous than illicit drugs. To take an obvious example, someone using barbituates under a doctor's supervision is putting themselves in a lot more danger than someone smoking weed.
A second point is that there's more need to regulate something that people think is good for them than something people think is dangerous. People are prone to thinking of drugs in a very Manichean fashion even if they are moderately aware of the facts about how the drugs function. Thinking of a drug as "useful but dangerous" and acting in accord with that thought requires a bit of cognitive sophistication and will power that most people lack. For that reason, allowing people to self-prescribe medication would probably end up having extremely negative effects.
Third, limiting access to prescription drugs while allowing the standard set of recreational drugs would avoid many of the costs of our current program of criminalization. Part of the reason that drug laws are so widely ignored is that there really are no (or few) substitutes for the recreational drugs that people use. So they keep using them, and we have the high cost of enforcement most importantly the harm to those who are prosecuted, or the victims of drug war related crime. If today's recreational drugs were legalized, while keeping prescription drugs limited to those with prescriptions, the prescription drugs wouldn't have the same incidence of illicit recreational use because of the availability of substitutes.
That said, I don't think the tension is really resolved. I ought to think about this more if I want to get it right.