When someone like a parent, teacher, or boss is angry, they may tell their children, student, or employee what to do, and then ask "Do you understand me?" They expect a response like this:

A: You are not allowed to go out with him again. Do you understand me?

B: (Looks angry.)

A: I said, "Do you understand me?"

B: Yes, I get it.

When English speakers ask "Do you understand?" or "Do you understand me?" it often sounds angry and impatient. If you want to know whether someone understands you, but want to ask politely, ask:

Does that make sense?

Or maybe:

Got it?