Right off the top, I DO NOT want to question the timing of this leak whatsoever. I see absolutely no connection between a link analysis program that begun in the NSA in 2001, and the recent nomination of the former head of the NSA to DCI. It would be ridiculous to even speculate that the leak of this highly classified program was timed to affect the outcome of upcoming Senate Intelligence Commitee hearings. NO PHREAKING WAY!
What the USA Today article is describing is a tool used by law enforcement (without a court order) to attempt to find additional bad guys who associate with a known bad guy. Let's say, you bust a guy for smuggling dope into the country and he has a cell phone on him. You seize the phone, and you copy the recent numbers and maybe even his entire phonebook from the phone down and submit it to a law enforcement data base. They throw those numbers in with everybody else's numbers and if you're lucky, some other agent is looking at a guy whose number was in your smuggler's phonebook. Then you call that agent up so that you can get some more information about your guy and vice versa. It gives you some additional avenues for investigation, but it isn't evidence of a crime.
So the big outrage of the day is that terrorist phone numbers are being collated and cross referenced to see if any connections can be gleaned from their communications patterns. There is no contention that the calls themselves are being monitored in any way.
The likely reason that this database is so large is that terrorists typically employ more elaborate countermeasures to detection than dopers do. For a narcotics investigation, it would be a waste to go any further than one level on these numbers; not so for terrorists. For example, a terrorist might call a number (perhaps a persian rug store) and ask if they have received the order for Mr. X. This rug store could actually be an communications intermediary who would then call an Al Qaeda guy to pass along a message. By analyzing the links several levels down, the government might be able to figure out if a couple of guys they suspect are terrorists are calling or being called by the same persian rug store. And if so, then it might be a good idea to focus some investigative effort on that store.
I don't call this an evil attempt by the Bushitler McHalliburton regime to crush civil liberties. I call it thorough investigative work that has the potential to yield positive results and identify previously unknown terrorists. Can you imagine knowing that this capability exists, that it has been shown to be effective in the past, and deciding that it is simply too politically dangerous to enact? Now that would be an impeachable offense.