Makes no different how you cut it, Sheppard is a huge drain on TTC bottom line that is taking away service that is badly needed city wide. It also taking money way from below the line projects.
How "huge" is it, do you have the dollar value of the annual subsidy?
My estimate: TTC's total budget (expenses) is about $1.7 billion. I did not find expenses for rapid tranbsit (3 subway lines + RT), but heard that it is about 30% of total. The total length of rapid transit lines is 80 km; Sheppard subway is 5.5 km, or 1/15th. Then, the cost of running Sheppard should be approx. 2% of TTC's expenses; or $34 million a year.
Furthermore, it does generate some revenue, thus the subsidy should be less then $34 million. How much revenue, depends on the allocation rules. Assuming that 50 cents per ride can be attributed to Sheppard subway, at 15 million yearly rides, the revenue should be about $7 million. Then the subsidy is 34 - 7 = $ 27 million a year. That's noticeable, but not "huge".
Looking from another perspective, it costs 11 dollars per resident of Toronto per year to subsidise Sheppard subway.
I realize that transit funding is tight, and even that expense is not helpful; but it is not "huge", and does not significantly affect TTC's other operations.