This got a little ranty, so tl;dr: if you want the rural areas to carry their own weight instead of being dependent on subsidies from urban areas, the best way of going about that is to invest in their infrastructure now so that they have the means to grow and prosper and contribute more to state tax revenues. In this case, the HSR wouldn't have been worthwhile to pursue if it didn't connect the Central Valley; it would have been a whole lot of spending for very little long-term economic gain in the short term (and outright economic loss in the long-term), as explained further below.

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"We've been fire-hosing money at rural areas for decades, if not longer."

Yes, because for decades - if not longer - they haven't had the tax base to support large infrastructure projects, by the very definition of them being rural areas.

"our system of government has one branch that over-represents the voices of rural citizens"

Clarification: it balances them against the overwhelmingly loud collective voice of urban citizens to protect against there being a tyranny of the majority. By enforcing strictly proportional representation, the rural citizens will get steamrolled time and time again. The United States went with a bicameral legislature - and the states followed with their own bicameral legislatures - because its founders recognized that giving minority voices sufficient representation to adequately defend themselves against majority interests is the key to long-term prosperity.

"If you expect people to pave roads and provide drinking water and put out forest fires out in Bakersfield, maybe you can spend your own money on it."

They do pay for those things through taxes. They can't pay as much as giant metropolitan areas, and thus do need financial assistance from said giant metropolitan areas, but it ain't like their residents are magically exempt from state income/property/sales/gas/alcohol/tobacco/etc. taxes, or state DMV fees, or the wide variety of other means by which the State of California collects its revenue.

"Keep up with this absolutist, ultimatum line of thinking, and you're going to lose."

Right back at you: keep up with this absolutist "you dirty farmers don't deserve to ride our fancy new train because we're richer than you" mentality, and you're going to lose. Your position is really the most selfish one possible: burn billions upon billions of dollars on a project that only benefits two already-overwhelmingly-prosperous metropolitan areas in the short term, thus doing nothing to account for the long-term growth of those two areas and their resulting need for their workforce to live further and further away from the city center to be able to afford rent.

Because really, in the long term, connecting SF and LA and Fresno and Bakersfield and (eventually) Sacramento and Stockton and Modesto and San Diego is a surefire recipe for eventual statewide prosperity. San Francisco in particular will have a lot of trouble continuing to grow economically (what with its rising housing costs pushing workers further and further away from the city center) unless there's a fast connection to cheaper places to live; with a high-speed connection to the Central Valley, you now have a more affordable home for a constantly-growing workforce. I'm less familiar with Los Angeles' dynamics in this regard, but I wouldn't be surprised if they saw similar gains. Meanwhile, those rural areas grow and mature and become less reliant on subsidies to operate. Win-win for everyone.

Sure, maybe that costs more upfront, and maybe it'll take a whole 3 hours to get from SF to LA instead of 2.5 (or whatever the actual numbers are, but IIRC even with the stops it's still less than 3 hours between SF and LA), but any sane and rational person would see that those costs are worth it if it means paving the way for California as a whole to continue to grow for another century the same way it has for a century already. Opposing the idea of the Central Valley actually having stops on the CHSR is the definition of irrationality: it'd still cost billions upon billions of dollars, and it ain't like a whole lot of people are clamoring to commute between SF and LA every day (both have thriving economies, and both have high costs of living, so there's no SF/Sac dynamic where people are willing to commute for 2+ hours if it means cheaper rent), so... what would be the point?

The only thing you'd accomplish by making the HSR SF/LA-only would be to extend a nice big metaphorical middle finger toward the Central Valley. If that's your goal, then you do you, but don't be surprised when the Central Valley votes against you while extending it's own middle finger in return.