Are they the bad guys? I'm not too sure. I think every character has his or her struggles and story, so that's why there are viewers who are pulling for Tori and people like me who are rooting for Sam.
The two kids who were picking on Kenny in the school's bathroom, they are Miyagi-Do, the so-called good guys.
Heck, I don't think Kreese is a real bad guy of the story. He truly thinks that Cobra Kai is a way of life, like Daniel truly feels that Mr. Miyagi's karate is the right way, well, after his U-turn in the last two episodes. the story tries to make clear of that.
I also think Kreese cares for Lawrence in his own weird, manipulative way, whereas Silver is a twisted psycho who bribed a ref and got Kreese in jail.
So, none of the main characters are real bad guys, except for one: Terry Silver.