It is not typical to write "thank you" on essays, but I can imagine myself writing it on an essay that was particularly well done and a pleasure to read. It would most likely come after a description of what was done particularly well done or why I especially enjoyed reading the essay. It would not be written in the absence of other comments. Unless this tutor always writes such a remark on papers, I would interpret it as high praise.

I would actually interpret it as 'thank you for completing the assignment and handing it in.'
i don't think it constitutes praise.

Oh, now I get it! That's why some of my students haven't been handing in their homework. I've been forgetting to thank them.

I'm inclined to agree that merely handing in an assignment has not (yet) become such a noteworthy occasion that it merits a "thank you" note. (Or has it?)

You could always approach the tutor and ask him what he meant by that note. In the absence of any other comments I'd be a little confused as well.

Thank you for your help. Although I have to admit that I am a bit biased, I choose the first explanation ;)...

Maybe he was simply somewhat absent-minded when he wrote "thank you" and really meant to write something along the lines of "good work"..?! :-)

It depends what level you are. Obviously you would not thank your 12 year olds for handing in homework, but when I did my MA, it was customary for tutors to sends email receipts after handing in work - complete with a 'received with thanks' comment.