Just to note: BNSF didn't pay for those road-rail separations; the city/county/state did (depending on what kind of road) with perhaps a little federal help.

LA and Orange counties have substantial local sales tax add-ons to help pay for transportation improvements. That's why they are adding HOV (sometimes with tolls) lanes and rebuilding freeways, and building a lot of road-rail grade separations. Without the local funds, state and federal programs, funded mainly from per-gallon gas taxes that haven't gone up since the early 1990s despite inflation and vehicles with better gas mileage, would be much less productive. Ventura doesn't have a local tax, so it has fewer road improvements (including grade separations) - it has to rely on the general state/fed programs. Whether one is proposed and they vote it in is a local decision.

Other parts of the US are more into toll roads than California. That's their decision. I prefer California's approach, but there certainly can be diff'rent strokes. It's particularly noticeable in Florida where, except for the Interstates (which are generally in poor condition), pretty much anything resembling a limited-access road has a toll. Even relatively short local connectors - be careful where you pull off the Interstate. Essentially all the roads into Orlando Airport, for instance, have tolls. So the planned train (NOT "high speed" - more like standard Amtrak equipment operated at the design speed) between Miami and Orlando should be a success - people in Florida, and tourists, are used to paying per trip for travel on other than local streets.