It would also scare people who are simply afraid of dogs, and be a major hassle for them, too.
You won't find a person more afraid of dogs than myself, and I've never been nervous about the sniffer dogs Metra has had at Ogilvie Transportation Center (nee North Western Station) for years now, dogs I pass by probably six days a week, 50 weeks a year. I'm not afraid of them because I'm reasonably confident that they're well-trained, unlike an unknown dog I might encounter on the street, in the park, etc.. And the dogs haven't been a "hassle" to Metra commuters, who just keep walking past them in the thousands without slowing down or even batting an eye.
You keep pointing out that no security measure can be perfect. No duh, but you know what, there have been laws against murder, rape, theft, etc. for thousands of years, and the fact that they still keep happening doesn't mean to any
reasonable person that we should disband the police and courts because they haven't been and
cannot be 100% effective.
Personally, I don't think there's anything wrong with
some additional security measures, so long as they don't cost too much and don't significantly inconvenience passengers. While I don't know about the cost, Amtrak's new program sounds like it's not too inconvenient. They aren't going to be creating jam-ups of passengers by checking
everyone, like they do at the airports, and I seriously doubt anyone's going to miss their train for the sake of a minute or two while someone rubs a wand on their bags and checks the wand in the explosive-sniffing machine. And there's no right to privacy on the
outside of one's bags.