"Why do you cry ?" Is a more general question to find out what causes a person to cry at a non-specific point in time. "Why are you crying?" Is to find out why they are crying in the present moment, the instance in which it is happening.

“Why do you cry” could be asking about the body’s system for crying…so the answer would be to do with the tear duct responding to a trigger. The pronoun ‘you’ could be replaced by ‘one’ for example ‘Why does one cry? Why are you crying is the correct way to ask someone to explain why they are upset.

Hello! Do you always means regular, permanent activities, situations while Are you describes activities which are happening rIght now, or during a specific period only. They are Present Simple tense, Present Continuous tense, true with each verb Many languages describes these tenses without any distinguishing, English as French describe them with special tenses

They have difference in tense. The first one is simple present tense. The second one is the present continuous tense which emphasizes that you are crying while the speaker is asking.

The first is present simple for GENERAL things, a fact about that person, and the second is present continuous, something which is happening NOW.