There's no proof to suggest they knew otherwise. Anything stated thus far is speculation. All that's been shown as "evidence" is a slide with company logos on it and some statements from the NSA which claims to collect "Facebook" data, which could really mean anything. Plus Google openly submitted a request to allow them to publicly disclose the number, type, and scope of NSLs it receives. I have more reason to doubt the Govt than these other companies.
Also, given the name "PRISM," isn't it pretty obvious how this program worked? Think about it... What does a prism do?
Meanwhile, Verizon and ATT have been completely silent and government representatives are making up new definitions for the term perjury.