Right, the better estimate of how economical transit lines are would be fares + gain in property value from the presence of the lines. (Or, to get the units right, fares/year + gain in locational rental value/year.)

Or to look at it another way: assume some genie offered to dismantle the NYC train/subway system for free. Assume you're the government and only care about maximizing revenue. Would that be a good deal? Of course not, even if the system wasn't self-sustaining from fares.