Last week's podcast on TWiT.tv, Security Now, Steve Gibson detailed how the NSA is obtaining data and how companies themselves are not participating or cooperating with them outside of court orders and requests.
Basically, they're tapping into the fiber optic feeds at the ISP level and splitting the light waves off (hence the term Prism) to their own routers and equipment. This is all done upstream of companies like Apple and Google. So the NSA is getting that data before it ever makes it's way to Apple, Google et al...
Skip ahead to about 57:31 to get the technical details of this.
YouTube: video
Yes, that was part of the report but while they could be most of the information at the backbone level they were not able to get all of it. The second part of it was filling in the missing pieces with alleged "backdoors" to the services servers.