Yes, it can definitely make your fever and general condition worse, especially if the Air conditioner hasn't had its filters cleaned in a while.
I will point out some of the reasons why AC is terrible when you have a fever - even if we are thinking of the clean AC of a car.
1) Your fever weakens your body, when you are under AC your mucosa (nostrils, eyes, mouth) goes drier being more receptive to bacteria and mites, for example, which can make your body worse as it will be something else for your already weak body to fight.
2) AC can also make you feel much worse as it makes already sick people mroe prone to getting into contact with dust, mite and other unpleasant odors. Also the air gets less fresh in areas where AC is on.