It's been known from the beginning Tor's design can't defend against these sorts of attacks.
Tor's purpose is to anonymize traffic. What is it good for, if it can't do that?
> A global passive adversary is the most commonly assumed threat when analyzing theoretical anonymity designs. But like all practical low-latency systems, Tor does not protect against such a strong adversary. Instead, we assume an adversary who can observe some fraction of network traffic; who can generate, modify, delete, or delay traffic; who can operate onion routers of his own; and who can compromise some fraction of the onion routers.
(https://svn.torproject.org/svn/projects/design-paper/tor-des..., Page 4)
I read an interesting article in the ACM last month, titled "Seeking Anonymity in an Internet Panopticon" (http://cacm.acm.org/magazines/2015/10/192387-seeking-anonymi...).
> The most well known global-traffic-analysis attack—"traffic confirmation"—was understood by Tor's designers but considered an unrealistically strong attack model and too costly to defend against.
They explain a number of attacks against Tor (both active and passive) and introduce Dissent, "a project at Yale University that expands the design space and explores starkly contrasting foundations for anonymous communication".
That's not the aforementioned Globally Passive Adversary. So by their own measurement the Tor project failed. That said, they took steps to mitigate the exact vulnerability these researchers exploited.
I am very surprised that a couple of guys at a university could do so. That's definitely within the realm of attacks that Tor was supposed to be secure against.