Facebook was listed as one of the companies participating in PRISM, with a specific start date. None of the denials or other announcements made by any of the companies the NSA seemed pretty sure were collaborating addressed why they appeared on that list. Until there is a good explanation for why the NSA thinks they were collaborating, denials ring pretty hollow.
It's not clear from the slides that the companies were "participating" at all. Further Snowden leaks showed that the NSA was cracking large internet companies' internal systems communications. PRISM doesn't necessarily need their cooperation at all.
Either the companies on the PRISM list are willingly collaborating, or NSA bribed one or more employees, or NSA attacked their infrastructure.
If it wasn't willing cooperation, then the PRISM companies have a security breach to solve. None of them have said whether they have such a breach or not.