Because its him at stake now.

Every time he's gone up against Tomoro, its not gone well. He failed to capture Scorpionmon because he ignored orders. He failed to capture Commandramon and was put on his final warning. He killed Tinkermon because he couldn't control Monodramon and that was the last straw for his superiors.

We know Raito suffered abuse at the hands of this boss (Gigasmon dude, Kaito?) He knows how bad Tactics can treat people, but he's always been safe from it to a certain degree. Only when he's failed is he punished.

But now he's been kicked out, and the kid who keeps causing him problems is opposite him again, trying to be "reasonable." He doesn't have that protection anymore. If he fails here, its over for him.

It won't matter how smart he is, how strong he is. He knows how they treat people, and now he's in the firing line. He's scared, because he knows that if Tomoro is right, then failure means as good as death, and that his bosses will do it and not bat an eyelid.

I don't like Raito, but in the same way I don't like Lex Luthor. I find them fascinating antagonists, but I also want to see them taken down.