This is one of those special circumstances that may lead you to think of the strictly functional aspect to futon covers. However, realize that there are many more esthetic purposes and aspects to this humble cover as well. Sure, they do protect your futon mattress from spills, stains and other wear and tear, but that is only half the story. They also can provide you with multiple pieces of furniture.
Think about it, how many times after the 'honeymoon period' of your guest room or home office furniture have you wanted to just throw it out and get something new? Well, that is certainly an option. However, this option will likely cost you a whole lot more than a cheap futon cover. These cost no more than $30-50 USD for the most basic type of cotton futon cover. For a leather one or something with a more detailed print or alternative material, like hemp, you will pay more. But, it is what you get for the money that counts in this case. And, in this instance, you will be getting what appears to be a completely new couch or love seat for way less than the replacement cost of the furniture itself. This much is obvious.
So, what about if you do have a more functional need in mind and you don't care about having some type of exotic animal print or college themed looking futon? Well, this is simple too. You can get a cover in a solid color that does nothing to greatly enhance your room's appearance and nothing to really take away from it. These types of futon covers are usually cotton or canvas and just sit like your grandmother's old plastic furniture covers, but without the noise. Okay, so they are not as ugly or tacky as those, but you get the point. This solid colored one is nothing fancy or stylish, just fine by me as well.
Back to the topic at hand here. With the types of chemicals used to process these futon mattresses, you never know what or if you will suffer from any type of allergies or other health problems. Not all futons are treated with the same chemicals, some have fire retardants that are required by US laws and regulations and others different chemical agents used in the manufacturing process.
Something that has been known for years and is simply becoming more talked about and discussed is this issue with mattress off-gassing. The name simply refers to the way that the chemical agents used in the manufacturing process are released into the air as gasses as you sleep with your head right there. There have been reported cases of severed respiratory and other health effects because of this issue. Now, imagine your newborn child sleeping on one of these mattresses. This has classically been more of a problem with the conventional mattress, but because of the popularity of the futon, these are becoming increasingly pointed to as well.
The types of futon covers that protect from this off-gassing would need to be sealing the offending gasses inside the cover itself. It is basically acting like a giant, impermeable zip-lock bag for your futon mattress. This type of futon cover is usually made of some type of plastic material, a polyethylene. It needs to be of a specific .5mils or it will not stop the gasses from seeping through. More recent advancements in materials and fabrics should help to create an even thinner plastic that provides at least as much if not more protection from off-gassing. In the future, hopefully with the help of the green conscious efforts we are making, mattresses can avoid being treated with such health offending chemical agents in the first place.