To be honest, once I get over the conditioning that it is only for criminals, I don't have a problem with fingerprinting itself. What I do have a problem with is that it is only for foreigners. The implication seems to be that it is the gaijin to be feared, and not their fellow countrymen. When if comes to foreigners, Japan seems to have a guilty-until-proven-innocent mentality. I know America has the same practice and maybe I would feel equally offended getting fingerprinted there, though with America, differences of race don't come into it.
In the explanation video, terrorist bombing attacks in America, Bali, Morocco, Spain and London are listed. Never do they talk about the worst terrorist attack in their own country in 1995, the Sarin gas attack, an attack on Japanese, by Japanese. I find the video quite condescending when they try to pass the fingerprinting practice off as being partly to protect the foreigners. Let's be honest Japan (or the government at least), you don't really care about the foreigners, you're too busy worrying about what you think we're going to do to you.
While I'm on the subject of safety in Japan, it is for the most part a very safe place to live in. The recent trend of random street slashings however is a disturbing one. Until this week, I wrote it off as being a "big city" problem and not something to worry about where I live. That has now changed. Two days ago, a girl from our school was chased down the street by an old man with a knife. He was believe to have been seen outside one of the school gates again yesterday.
Japan, is it really US you need to worry about?
j donuts has put together a great post linking to other people's thoughts on this matter. It's a really interesting and somewhat scary read. You can find it here.