Perception, don't blame the ACLU or the Quakers.
Blame the Bill of Rights. It is the Bill of Rights that give the gaurantees that you say help the terrorists.
The right that people have to express dissent is in the First Amendment. The protection against unreasonable search and siezure and the right to counsel are in the 4th and 5th amendments.
Of course there is an attempt to fix the problems in the Bill of Rights as reported by the Onion
http://www.theonion.com/onion3847/bill_of_rights.html
Which says
"As visionary as they were, the framers of the Constitution never could have foreseen, for example, that our government would one day need to jail someone indefinitely without judicial review. There was no such thing as suspicious Middle Eastern immigrants back then."
But, the Quakers do not pose any risk of terrorism. There is no reason for the FBI to investigate them unless the government is trying to stifle dissent.
But why would they want that?