HSR is California was always a bit of a gamble because there's three mountain chains to cross between LA and SF, which makes for expensive mountain crossings. But I'm perplexed as to why they're having cost overruns in the flat Central Valley.
After the NE Corridor, a Chicago hub network would make the most sense for high speed rail. The Northeast Corridor is already profitable (in isolation), but is also the best spot for HSR, so for another network one shouldn't expect profitability from day one.