Doesn't sound good at first glance. In defense of their actions is that by studying different groups (and I mean that in the mathematical sense) you will make whatever you are looking for stand out much clearer. Creating patterns of each group might make forecasting their actions a bit easier and be able to pick up an unknown group within the general population.
Just my thoughts.
"In all three cases, after other Homeland Security Department officials raised concerns, copies of the reports were destroyed. The agency also held a workshop on intelligence-gathering “while ensuring the protection of civil rights and civil liberties”
Someone made an error. They corrected themselves. iow, nothing happened.
It's great that they corrected themselves and all, but why didn't this come out in public? It seems to have taken an FOIA to get it out there.
Also, the "error" is particularly egregious and Stasi-like: collect info on people doing something legal, nay, constitutionally protected. It's also very typical for US Secret Police to do. The COINTELPRO program infiltrated Quaker organizations in the 60s, some DoD office did it before Gulf War I, and someone seems to be trying it today:
http://www.afsc.org/ht/display/ContentDetails/i/5264/pid/268
I suspect the Secret Police tries to infiltrate Quaker organizations because it's so easy: they welcome just about anyone, and do all their work out in public, unlike less trustworthy organizations like the DHS and TSA.
EDIT: Actually the incidents in the article are fairly tame. There are much more egregious examples.