Is it appropriate to reply every time to a professor's "thank you" email?
Email exchanges need to end at some point.
If the professor's email is a simple receipt of correspondence, then I don't think there's a need to reply. However, if the professor has initiated a larger email then a reply is probably appropriate. See these examples:

Thanks sent as a form of receipt:


  Student: Hi Professor Smith,
  I've run the analyses you have suggested (see attached),
  Cheers,
  Mike


Then the professor replies:


  Pofessor Smith: Thanks for that


In this case, I think there is no need for the student to reply "You're welcome".

It wouldn't be a big problem, but it would be mildly distracting for the professor. Email exchanges need to end. The professor's "thank you email" was already a confirmation email indicating receipt of your original message.

Thanks sent by professor as part of a larger email initiated by the professor

Imagine the professor sends you an email that provides detailed information that also includes a thank you.


  Professor Smith: Hi Mike, well done on your work in the lab the other day. You did a really good job of fixing that equipment. I really appreciate it.
  Cheers,
  Professor Smith


In that case it might be appropriate for the student to reply: "you're welcome".