I am of the opinion - nothing more - that they were capturing the connections between known and (previously) unknown individuals for the purpose of building a network diagram of al Qaeda operators and sympathizers, whether internationally or here in the US.
You might be right, but that would be a darn weak protective/preventive measure.
As others have said, the only ralistic approach to communications is to assume that 100% of the contents can be and is intercepted - act accordingly and you'll be fine.
No, because a pattern of communication would present the probable cause necessary for a more (rightly) intrusive monitoring program against suspect individuals and organizations using a FISA warrant.