What does not make sense? What more specific? Perhaps you want to react to some existing comment on this page?
Please see the answer by endless_sleeper and the Tips and notes about Czech cases and the free word order. Because the verb is singular "žere", it is coupled with a singular subject. Therefore the subject cannot be the flies. If it were "What do flies eat?" it would have to be "Co žerou mouchy?" with a plural verb.