- The companies are lying.
- The government has infiltrated these companies and developed backdoor access the executive team is unaware of.
- The government is intercepting traffic en-route and doesn't need cooperation of the companies.
- The government is confused on their talking about about what they're confirming here and PRISM has been misinterpreted by the press.
#1 is possible, but implies that there exists a National Security Letter-like mechanism that can coerce this kind of public behavior. I find that unlikely but certainly not impossible; that would definitely be a concerning outcome.
I think #2 is unlikely. There's an interesting passage in the original Washington Post article, though, about how they want to be careful to protect the identities of the cooperating companies so as to not "damage their sources". A simple reading of this is that the companies might pull out if they're publicly exposed as cooperating. However, since they appear capable of coercing cooperating anyway, a slightly more tin-foil-hat reading is that their access is less straightforward than asking Page and Zuckerberg for help.
#3 is probably happening regardless of whatever cooperation the companies are providing. However, if that's the extent of PRISM I think it says interesting things about the likelihood that RSA has fallen. Is that likely? I have no idea. It wouldn't be unprecedented compared to what the NSA and its predecessors have done historically, though. It's worth noting that the NSA hasn't approved asymmetric crypto for protecting classified data. (http://en.wikipedia.org/wiki/NSA_Suite_B_Cryptography)