My kids live out there so I have been out in the Bay Area quite a bit. I can't think of any area that Caltrain serves as an unsafe area. Ithink the best spot for Caltrain is the Santa Clara station, one of the oldest extant and still used stations in the whole of the US. Go from mid morning to mid afternoon for best light, Early AM is likely to be hazy or even foggy. There you will see Caltrain, including the Baby Bullets whizzing by at speed ( stand well clear of the track area when that happens) UP freight with a few SP or Rio Grande units that work South San Francisco, Amtrak and ACE commuter trains and one of the older SP towers at the north end. If you go one station farther south that will be San Jose a wonderful Beaux Arts-Spanish Mission station though you may be shooed away from the platform area by security. If you walk about one mile to the south of the station you can access a safe bridge with a great view of the station and yard and also the VTA light rail station. Speaking of stations take a look at the Burligame station, Spanish Mission, Menlo Park, Victorian ginger bread. Palo Alto, late beaux arts and if you get off in Palo Alto walk about a half mile north of the station to an older girder bridge much used by the SP as a photo op in the days of steam. The original, EL Palo Alto, a tall redwood, the High Tree, is right next to the bridge. Best time for these stations is mid morning after the haze has burned off. You mentioned safety. There is one spot Caltrain passes through in the Hunter's Point section of SF, the only part of the city with industry and a working port facility. Caltrain and an adjacent freight spur line passes through this gritty area. if you like trains in an industrial setting, and two long bridges, this is a good spot. Take the T light rail from Caltrain terminal to Innes Ave., I think that's the stop, and walk about one mile west. if you just want to glance at that location look to your left as the train out of SF travels south and you will see it and perhaps spot the local freight that works the docks. If possible ride the bike car on the trains pulled (or pushed) by the older F40 locomotives. They have a window on the door you can play second engineer from. The newer Baby Bullet trains don't have that door. When you get on the train at Caltrain's SF station the bike car will be the one closest to you and it has a bathroom, too (unlike SEPTA Trains). I love rail fanning the Bay Area. If you want some tips on other good spots in that area let me know and I'll point them out.