It's mostly just a matter of what is more socially acceptable in our culture. Most people are of the mindset that an occasional drink or two is perfectly fine while a much smaller portion of our society is ok with the idea of someone having an occasional joint. Realistically, while they're both bad for you, they aren't terribly dangerous if used responsibly and in moderation.
This is an excellent video on the known negative health effects of marijuana, which I suggest for anyone that tend to take either extreme on the topic.
While I'm not interested by or fond of marijuana, I do generally think we would be much better off by legalizing, regulating, and taxing it like we do alcohol.