"You're welcome" does imply an acknowledgment that you actually have helped the person, but it's never rude to say it. If you want to make it sound like you haven't been in any way bothered by helping, you can say "no problem" (this is an extremely common response to thank you") or "don't worry about it." If you want to say that you enjoyed helping the person you can say "my pleasure" or "happy to help"

It isn't too polite, but you will usually hear "you're welcome". "You are welcome" if often used as a response to a very big thank you, but "you're welcome" is fine here, too. "Thanks so much for helping me with my English. "You are welcome."

"You are welcome" is a neutral way to reply to a person when they thank you for something. It is definitely not "not too polite", in fact it is preferable. In informal situations you can say "No problem" or "No worries" Hope this helps :)