Summarize:

Invest in a futon cover to keep your futon clean. You can buy a cover online or at a local department store. The cover should protect the futon from stains and spills. You should wash your futon cover with your laundry a few times a month. If you use a cover, do not leave it on your futon all the time. When cleaning the futon, remove the cover for an hour before you begin cleaning. This will give the futon a chance to air out. If at all possible, use a frame for your futon. The closer your futon is to the floor, the more susceptible it is to dirt and debris. If you keep your futon on the floor, you will have to clean it more often.
Place a cover over the futon. Air out the mattress on occasion. Avoid placing your futon on the floor.