http://www.slate.com/blogs/future_tense/2013/07/31/xkeyscore...
It's also more efficient to just tap the connections of the users' ISPs, rather than tap each home. And since they're tapping backbones, a VPN will only help some. It'll limit the ability for them to easily search you via IP - they'll need to try to distinguish your traffic from the other users on the proxy/VPN. I didn't see anything about correlating timing information, and it'd seem like that'd be a much more difficult thing to analyze versus indexing HTTP requests.
But if you read the slides, the instructions to operates are VERY clear to never use this data (passwords and such), but only pass it on to TAO. I'd guess they'd want to be really certain before doing something active/noticeable which might involve spending some sort of identity.
Remember, most of these things have as their only threat model someone trying to gain access from the Wi-Fi side before authentication. I doubt many vendors seriously consider questions like "can the cable connection to the ISP be used to take over the router?" or take steps to prevent it. For many devices, that sort of access could be considered as a potentially legitimate feature (think, customer support and remote diagnostics).