"Ty jíš sýr?"

Translation: Do you eat cheese?

[Rachel730135]

How do you know it is not: Are you eating (the) cheese?

[Paul440375]

You don't, it can mean both things. You can know it only from context or you can specify by for example adding "teď" (now) to the sentence, so that it is clear that you are asking: Are you eating the cheese now?

[kacenka9]

Are you eating cheese is also acceptable reply.