If you want people to prefer to take transit, and you should want that, you need to deal with the lack of a social contract on public transit. That means, in other words, that behavior not tolerated in a private business (such as a bar or restaurant) can't be tolerated on public transit either.
For urban liberals, that means confronting some uncomfortable choices. A public space (and transit is public) is supposed to be open to all, but if we want public spaces to be livable, that probably means smells and behaviors are more tightly regulated in public, either through direct enforcement by transit police (unlikely) or more social pressure (also unlikely).