The original Baron Heinrich Zemo fought Captain America in WWII, and his son Baron Helmut Zemo also fought Captain America, allying with various villains, and also tried to restore his father (Heinrich).
This is where it gets interesting (and relevant):
[Zemo] organized a new team of Masters of Evil when the Avengers and Fantastic Four disappeared during the Onslaught crisis and were presumed dead. These Masters of Evil took false identities and called themselves the Thunderbolts
He leaks the true identities of his villain!hero team, and is subsequently betrayed by them. A few body swaps, and reality jumps later he returns to lead the Thunderbolts, still secretly trying to take over the world (to save it). Along the way he ends up manipulating the US Government, and some other characters.
As a result of Civil War storyline, Iron Man asked Zemo to begin recruiting villains to his cause, which Zemo had begun doing some time before, unknown to Iron Man.
So whilst you might not have seen him in the TPB, Zemo is the leader of the villains recruited to track down unregistered superheroes. They are seen in the sewer scene, fighting Spider-Man before he is rescued by Punisher (if I recall correctly).
As it stands, the TPB only covers Civil War #1-7, without all the side stories. More TPBs exist covering Civil War.