I intended to write a post debunking the myth that high-speed lines do not pay for themselves, but Paulus Magnus has written one instead. He posts the revenue and net income figures for the mainland JRs, SNCF, DB, and RENFE. All but RENFE have positive net income, and even RENFE has positive EBIT.
The only thing I want to add is that there’s a myth going around that the Shinkansen isn’t really profitable because the government wiped its construction debt. While it’s true that the government wiped JNR’s debt, that debt was predominantly operating losses before restructuring; since JNR got few subsidies, it had to keep borrowing to cover its losses: see pages 46 and 88 on this PDF. Construction was only one eighth of the debt burden, and that part the JRs did have to pay. In other words, the government really just subsidize JNR’s operating losses from its inefficient pre-restructuring days.