Obviously yes, you have to since the vast majority of expenses (>70%) are fixed costs. If you only exclude them and only look at marginal costs, they're profitable.

But you cannot run a transit system on marginal costs, so using that comparison is also misleading.

Thought experiment: What would happen with total profitability, given positive marginal unit economics, if readership were to greatly increase?

The usual rule of thumb is that fixed costs of public transit are covered by increased property values. It could mean a private transit company developing the areas around stations (as it often works in Japan), or it could mean the government getting more money from property taxes. Or it could even mean more money from income taxes, if the transit project stimulates economic activity.

If a transit project doesn't increase property values enough to justify the investment, or if the entity funding the project cannot extract that value, the project rarely makes sense.