2. There have been ongoing efforts to improve equity, including Go passes for students and low-income workers. Clipper START offers 50% off for low-income riders, youths can ride for $2/day now. Side note: subsidies and programs like this decrease farebox recovery ratios, which is why transit covering its own costs is not necessarily the end goal. In fact, the decline of commuting for tech/knowledge workers (many who now work hybrid or fully remote) has meant that less-privileged workers have started making up a larger share of Caltrain ridership.
3. The new electric trains are a lot quieter. There's ongoing, long-term projects to grade separate the remaining at-grade crossings (of the 113 crossings, 41 still need to be separated).
4. Arguably, the stations were directly responsible for the land being so valuable. Many peninsula downtowns and sometimes entire cities were built around the train stations, 100-150 years ago. Pre-pandemic, some of the most expensive apartments were the ones near the train station. Sure most of them also had the benefit of being close to downtown restaurants, but there were also big developments around Lawrence station which has basically zero local services aside from the Costco and the train station.
Of course this was mostly in the past, but downtown areas continue to be congested and the only way we can keep building high-density housing is to have good public transit. In the long run, the train provide immense benefits to the cities that host them and removing it would be shortsighted.