Many hotels have online reservations and accept credit cards. Smaller hotels may only accept cash. Online travel sites are also great resources and many hotels are registered through them.
Room tax is about 7 percent and may be quoted in the room price.
Cairo does not have many boutique hotels or B&Bs. If you can find a bed & breakfast, it can be a refreshingly personal environment to explore a new city. Though a B&B may be more expensive then traditional hotels, occasionally they are cheaper then the surrounding locations given the inclusion of a meal and the luxury of the environment.