Well, after that, I'm guessing the reason would be because the people that're the supposed targets of such action (the Terrorists, if you will) would then be able to take action to circumvent it (ie communicate more via mail, try to obtain information on what key phrases and such trigger additional surveillance, come up with better codes for phone communication) whereas by keeping the project in the dark, it would lure such suspected terrorists into a false sense of security and prevent them from taking such measures.
And of course if you then expose those methods in an open trial, to implicate one particular terrorist, then you make circumvention of those same methods easier by others with motive to avoid the surveillance.
All of it makes sense from a law enforcement view. In a way, it's one of those moral questions - is it worth it to break into someone's house if there's the possibility of saving a life? I can probably think hard enough to come up with some tough dilemma, but I think the deal here is that you're faced with a conflict of possibly saving an unknown number of lives while opening civil rights for everyone up to an unknown number of abuses, or possibly securing that unknown number of rights for everyone while sacrificing that unknwon number of lives. And as long as the government doesn't suspect you of anything, and you fit in with society, you don't have anything to fear.
Perhaps you have to suffer some inconveniences from additonal security checks - but what's a few minutes' time? After all, sacrifices have to be made for freedom. If you're dead, it's kind of hard to enjoy your freedom...and the US has one of the higher standards of living in the world.
