Depending upon your needs, looking for the right type of futon cover to protect your mattress might be a toss up.  There are different types of slipcovers for different types of requirements.  For example, if you use your futon as a secondary seating arrangement when you are entertaining, then getting a cover that will protect from spills and stains is probably the most important.  If you are using your futon as a bed, then you need not worry about design, patterns and the like as it will be covered by your bedding.

If, on the other hand, you are looking for protection from dust mites, pollens and other allergens, then a mattress encasement might be what you need.  These provide for a fine level of screening so that the small (often microscopic) organisms cannot be breathed in.  A child who is very sensitive to airborne allergens will definitely do well with a mattress and pillow encasement for best protection.