I'm not sure about transit but when I (EU citizen) have been to the US they took all ten of my fingerprints, and this has also been the experience of my friends.
(Incidentally, my own government doesn't even have any of my fingerprints...)
Your handle suggests you're Dutch: every Dutch passport issued in the last decade (and hence, I think almost every current valid Dutch passport?) has your fingerprints. In fact, the Netherlands is the only EU country so far (I think) that's storing them all together centrally, not just in the passport.
That article is from 2009. I believe a few years later fingerprinting was scrapped again due to public backlash. Now they're implementing it again due to EU regulations.
I wouldn't be so certain that your government does not have your fingerprint... if it's European you can bet that at least your secret services have it as part of "we spy on your citizens, you on ours" agreement.
Of course they do - at least in Germany. Your biometrics are part of your personal ID and passport. It is only thumb and index finger though plus facial scan / photo.
Incidentally, when EU countries introduced biometric passports in mid 2000s, USA was one of the first countries to actually require the fingerprints and not accept older but otherwise valid documents.
(Incidentally, my own government doesn't even have any of my fingerprints...)