Most public goods don't benefit everyone equally; that's never the case, and that's fine.

My house has never been on fire (knock on wood), but I'm perfectly happy that my taxes pay for a fire department. I don't often use the park up the street that's currently undergoing a massive renovation/rebuild, but I'm happy that my taxes are paying for the renovation. I don't drive on every single road in the city, but I'm glad my tax dollars make it possible for people to get around even in places where I don't need to go. I don't have kids (and don't plan to), but I'm happy that the taxes I pay go toward educating the kids who live here.

Many public transit agencies are run at a loss; I'm absolutely fine with my tax dollars making up the difference. From there it's just a matter of degree: is it fully funded by taxes, or still partially funded by fare revenue? I'd be fine with the former, too.