This question is hard. At first glance, they are nothing alike. Even after giving it some thought, I could only come up with a few similarities.
I'll start with some surface level, concrete similarities. First, both men are fathers. Additionally, both men are fathers to daughters. Atticus has Scout, and Shylock has Jessica. Beyond that, both men love their daughters. It's clear that Atticus loves his children based on how he treats them. Shylock may not be as endearing as Atticus, but he does want the very best for his daughter. He wouldn't do that, if he didn't love her.
Second, both men believe in the justice system. Atticus is a lawyer, so that's an easy one. Shylock as well, believes in the justice system. That's why he takes Antonio to court for his pound of flesh. Shylock could have hired some "hitmen" or "mob guys" to take care of it for him, but he doesn't. Shylock thinks the justice system will work. Atticus does too.
Third, both men lose their court cases. Tom Robinson is found guilty despite Atticus's attempts to prove otherwise. Shylock gets neither his money or his pound of flesh. In fact, he winds up broke.
Fourth, both men honor the court's decision. Neither man is happy about the outcome, but both men accept it.