Though this season has been losing some steam recently, I think this has been one of the better seasons in a long time.
The question, why is Tony a villain?
I have a theory of what is going on with Tony.
Tony is on a revenge rampage that started when he tried to kill Henderson in Season 5.
This â€œgroupâ€ is connected with the events of that season and Michelleâ€™s death, and Tony is trying to get to them.
He used his â€œrecruitmentâ€ after his fake death to try and get closer to these people.
Unlike Jack, who only goes so far over the line out of revenge (see Nina), Tony is totally consumed over it, and no longer cares about wrong or right. He is willing to gun down or kill FBI agents all in the name of his revenge.
So in essence, he truly is a bad guy or a terrorist, but his motives have not been revealed yet. His motives are this gray area of morality (at least to him), but he is very much in the wrong.
I think this is supposed to be a contrast between Jack (the â€œheroâ€ of the show) and Tony. How Jack reacted and who he became when his wife died, versus Tony.
Jack will eventually have to put him down, because while he understands Tonyâ€™s anger, he cannot justify Tonyâ€™s actions.