If you asking someone what they are eating for lunch at that exact moment. 'What are you eating for lunch ?' If you are asking someone what do they usually eat for lunch you can say 'What do you eat for lunch?'

Both are correct. "What are you eating for lunch?" asks about the future, ie. the next time someone has lunch. Lunchtime is in the future. "What do you eat for lunch?" is a general question. You're asking about what someone usually eats.