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.

How is it misleading? Taking the total cost to operate and dividing by the number of rides tells you what it costs per ride.

I’d be more interested to know how so many people are paying less than $1 for a mini trip when the fare is closer to $3.