Yep. He's a twofer. After starting off as a victim of Ferneze's prejudice, Barabas quickly transforms into a villain who spends the rest of the play gleefully plotting against, oh, basically everyone else. Sure, there are reasons to sympathize and sometimes even like Barabas, but he's definitely a bad guy.
Ferneze is a bad guy, too, but in a different way than Barabas. He may not go out and poison nunneries or strangle friars, but there's no doubt that he does less-than-moral things. Under the pretext of good governance and Christian piety, Ferneze swindles the Jews out of their property. He makes a deal with the Turks, then breaks it.He agrees to help Barabas in his plot against the Turks, then betrays him at the last moment and gets Barabas killed.
The interesting thing here is that the very things that make Ferneze a bad guy are also the things that make him a very effective governor. He may be hypocritical, sneaky, and plain unfair, but at the end of the day, Ferneze's plan is to defend and unify Malta. And it works.
However unscrupulous his methods, Ferneze does in fact find the funds to pay off the Turks (even if he eventually decides to side with the Spanish), and his ultimate betrayal of Barabas soundly eliminates the two major threats to Malta's safety: the Turks and Barabas himself.