The Constitution in Wartime
Findlaw has an excellent essay discussing the history of law in wartime. The author makes the point very elegantly that inter arma silent leges (usually translated "in time of war the law is silent", but I prefer "in the face of arms, the law is silent"). Richard Stallman has an essay on a similar theme, not quite as good, but still worth reading.
Basically, now is when it's most important to have groups like the ACLU. Like most liberal groups, they're being attacked as unpatriotic, but considering we have cases like Korematsu on the books and not overturned, having groups that will watch out for violations of our rights and raise public awareness is important.
And it's not like it's only leftist groups fighting for these thigns, either. The article in the post didn't mention things like the Alien or Sedition Acts, but some of the languge in the bill Ashcroft is trying to ram through congress. There was a coalition of groups from the ACLU and gay rights organizatons to the NRA and anti-aborition activists all united in opposition, saying that we can find ways to protect the security of citizens *without* depriving them of rights.