What would be interesting would be to investigate how much the highest executives for each of these transit authorities are getting paid (yearly, and in a per passenger cost..) And comparing the average employee salary to say the median family income in the various jurisdictions.
Unjustified salaries, benefits and retirements are likely the biggest factor in these losses. And in my opinion, are simply open embezzlement of public money - taking that which there is absolutely no rational justification for paying that rate of salary and benefits.
As for the supposed land and business value increase from light rail stations - how much do they deduct for all the land the stations, rail, support infrastructure and parking? How much for the original land purchases? All of that should be subtracted (not to mention the yearly losses and whatever unfunded liabilities are also unaccounted for) from the ‘increased land values.’