There’s a pervasive myth that the Hong Kong MTR is profitable only because the company’s real estate investments subsidize the train operations. For a trivial refutation, go to the MTR’s 2008 financial statement. Operating income was HK$13,995 million, which breaks down as $4,670 million from real estate development and $9,325 million from railway operations. Net income was $8,280 million; the statements do not break down depreciation, amortization, and interest charges according to whether they come from transportation or real estate, but the operating profits from transportation would’ve been enough to cover everything.
For a comparable link to Japanese private railroads, another source of the myth of development-subsidized transportation, see this article from JRTR.