Yes, responding with "you're not welcome" when someone says "thank you" after helping you can be considered rude or impolite. The phrase "you're not welcome" is a direct way of expressing that the person's thanks are not appreciated or acknowledged. It can come across as dismissive, ungrateful, or even hostile, depending on the context and tone.
In most cultures, when someone says "thank you," a polite response would be something like "you're welcome," "no problem," "it was my pleasure," or any other positive acknowledgment of their gratitude. These responses show appreciation for the thanks and reinforce a sense of mutual respect and goodwill between people.
If someone consistently responds rudely to your expressions of gratitude, it may be worth considering having an open and honest conversation with them about how their responses make you feel. Effective communication can help resolve misunderstandings and improve the overall dynamics of the relationship.