If I had a few million dollars to run compromized Tor nodes, and the ability to subpoena (and gag order) any Tor node operator in USA, UK and a couple of other major countries to give me their keys, I would be able to easily de-anonymize a large portion of the network.
It is commonly assumed that the NSA/CIA run a substantial portion of the exit nodes. Morever, they are a global adversary (one Tor is not designed to defeat).
> Critical mass of targets use Tor. Scaring them away from Tor might be counterproductive.
In other words, they'd rather only have to break one anonymization service instead of five.