Is the doubling of annual patent protection fees upon late payment considered usury (riba)? Is it permissible to work in an office that deals with such a practice? And does the ruling on usury apply to late renewal fines for car licenses?

The annual patent fees are a charge for protecting a right, and increasing them due to late payment is prohibited usury (riba). As for your work in the office, if it is in a permissible field and you have no connection to stipulating the penalty, then there is no harm in it. As for the late fines imposed by the passports and traffic departments on those who delay, these fall under the category of financial discretionary punishments (ta'zirat maliyya). There is a disagreement among scholars regarding their permissibility. Ibn Taymiyyah and Ibn al-Qayyim permitted them, and the Islamic Fiqh Academy also approved them for the benefit of deterring offenders.