What is the cryptome document for prosectors that you refer to?
http://cryptome.org/2013/09/computer-forensics-2013.pdf
http://cryptome.org/2013/09/computer-forensics-2013-hoax.pdf
That's a pretty obvious hoax, detective "Stu Pitt" and "Laughlin Foo". It's good that it was quickly labelled as such.
All people are doing is applying the same logic and standards governments and spy agencies do. Is there any evidence that the WHOLE of the US and rest of the planet's public are traitors and terrorists? No. But they could be, right? Best not take a chance, right? "We" can do it, it is possible, so "they might be doing it. And so on.
So, the NSA can or could compromise tor nodes, we know it is possible, so why take the risk? Especially if you are, say, Snowden or a freedom advocate.
It's probably good to insist on sources. I should've provided one originally anyway: http://www.nytimes.com/2013/09/06/us/nsa-foils-much-internet...
1. VPNs using PPTP
2. VPNs using OpenVPN
1) should not be used anymore, it is more vulnerable by design (intercept the initial handshake and you're set; the NSA slides referred to a feature "Show VPN startups", which is probably what they meant by that).
So my guess is that when the say "we've cracked VPNs", it's probably PPTP VPNs, but then again, nobody knows for sure.