I really don't care if the FBI is spying on possible threats to national security. Actually, I don't really care if they are spying on me.... I think they should be allowed to do what they need to protect the people of this country. However, I do disagree with any possible operation like the one in Bourne Ultimatum. I think the government should be allowed to do what's necessary to protect the country, short of physical harm. A trial should precede any of that.
The FBI people have probably already sworn themselves to secrecy concerning gov't operations. So they probably won't be telling the nation about a 14 year old couple repeatedly saying they love each other on the phone, or your grandmother's complaining about her incontinence.