I wasn’t aware of any complaints about the trains for years prior to the passenger rail company joining in; it was only when trains carrying people entered the picture that the protesting began claiming that these trains are unsafe and unwanted, but the arguments I’ve seen on signs etc. aren’t related to passenger rail specifically. Perhaps the passenger rail stoked fears that the rail traffic would expand further.
Every railroad crossing is clearly marked, with multiple redundant flashing signals and moving barriers that get directly in the driver LOS. I’ve seen drivers push through the barriers to squeeze just ahead of or behind a moving train a handful of times in the past five years, but that’s about the same number of blatant red light runners I’ve seen in the same.