"What's your point?" means "for what reason do you say this?" You say this when you understand what the person said but you don't understand why he said it. Say "What do you mean?" when you don't understand what the person said, in order to invite him to say the same thing again using different words. Neither question is rude. These expressions are appropriate and polite so long as your tone of voice is sincere. You will need these expressions in conversations where you discuss complicated issues. If you're worried about coming across as rude, add the word "please": "Could you please explain your point?" or "Would you please explain more what you mean?"

“What’s your point?" is a way of asking someone to get to the main idea or purpose of what they're saying. However, it can come across as a bit rude or impatient. On the other hand, "What do you mean?" is a more polite and neutral way to ask someone to clarify or explain what they are saying. It shows you're interested in understanding their perspective. For example, if someone starts talking about random things, and you find it irritating, you can say, “What’s your point?” It can also sound more neutral in a friendly debate. You can ask “What’s your point?” if they’ve presented a bunch of arguments and you don’t see how the ideas connect. However, “What do you mean?” is more broad. You can use it in the situations above, and it will sound more general. You can also use it when you don’t understand a word or phrase.