Social factors for one thing. And the person drinking is more likely to injure you than they normally would be, the results of which are worse than a bit of passive smoking. Also, the drunkard is a threat to himself and others, which can cause panic amongst other passengers and staff. For those reasons, I'd be happy to ban alcohol from the railways except when served as part of a meal service.
Smoking has worse long term effects, but a bit of passive smoking's not going to kill you, whereas a drunk person might. In the long term, yes smoking has worse complications but in the short term there's probably not that many problems. That said, it's dirty, unpleasant, and you walk away smelling of tobacco. And, again, you're in a confined area. Of course, smoking should be banned on trains, but I think I see where djw is coming from on that one...