I read the brief article, and read RFC5961, and here's a quick summary:
A TCP connection is uniquely identified by the combination of: Source IP address; Destination IP address; Source port number; Destination port number. TCP also has a sequence number, which helps reorder packets. It also helps prevent spoofing, but spoofing is still possible. Any computer on the internet can craft a packet to send to a Destination IP address and Destination port with all the other fields spoofed. A spoofer cannot receive a reply (the Destination machine will send any replies to the indicated Source IP address, which the spoofer cannot see).
So, it's possible to inject SYN and RST requests into valid streams, shutting down other people's connections (although you couldn't be sure you've succeeded). RFC5961 tries to prevent this by adding some cases where the SYN/RST are not treated as valid, but instead it sends a special ACK to the source requesting confirmation. To avoid denial of service, these special ACKs are rate-limited to 10 per 5 seconds. Note these special ACKs are only generated if the SYN or RST look "nearly" valid based on the sequence number, otherwise the RST or SYN is ignored.
And that's what they discovered is the problem--open your own connection to any Destination which has long-term connections (and they picked a USA Today website, but anything would work), and every 2 seconds try to get it to generate those special SYN/RST ACKs. If it's not under "attack", you'll get your ACKs.
Then, spoof billions of packets using a chosen source IP address (and loop through all sequence nums and port nums) and guess the dest port (say, 80).
Now send a little traffic to the Destination on your valid connection to try to get these special SYN/RST ACKs. If you don't get your ACKs (due to the global rate limiting), then you "know" that you've stumbled upon a valid combination of Source IP/port and Destination IP/port and sequence number, so you know who's talking to the Destination machine. If you've picked a Source Address and port number not connected, then these special ACKs don't get generated, so your slow traffic generating these ACKs will not be rate limited, so you can tell this Source IP/port are not connected to this destination IP/port.
So RF5961 turns a pesky annoyance bug into a bug where its possible to determine who's connecting to a particular website (although time consuming).
RFC5961 should not do global rate limiting--it leaks important data.