Either way, in socal the metrolink trains operate at grade going pretty fast up
  to 80mph and you don't see so many accidents. I'd blame some other factor over
  the fact the train runs on the surface behind a gate.

Such as? Brightline has the worst record in the country. In the Bay Area Caltrain runs similar speeds, for a similar length of track, and still manages half the annual deaths. And, yes, Caltrain deals with people on the tracks fairly regularly. And, yes, I know nothing's perfect – someone just managed to drive right into a BART train last Monday. Regardless, Brightline is doing a worse job than any other rail company and they're resistant to any obvious (and relatively low cost) improvements. Caltrain, while already having a better safety record, is moving towards grade separated crossings to safely facilitate higher speeds. Grade separation is way more expensive than the shit that Brightline is refusing to do.

Is it? Most, if not all, of the rail I've seen in Europe is either grade separated or access restricted in some manner. The UK in particular stands out to me.

Brightrail runs 130 kph trains through populated areas, mostly at grade including crossings. Caltrain runs a comparable system in length and speed and sees roughly half the annual deaths. Do you have a better explanation?