It's up to the individual...
People rep for different things so naturally people will have mixed opinions on whether someone should be thanked for it. Mostly I take it as a "good job" acknowledgement from the repper ...for that I thank the person who bestows the rep for their acknowledgement.
My initial instinct when I first got repped was that it would be rude or kind of jack assish to not even acknowledge the act of someone repping you.
I mean, you make a good play in some sport and people around you say good job or great play...shouldn't the natural response be "thank you" to that?
Rep doesn't seem very different concept-wise from that IMO.:2 cents: