It also means "think nothing of it." A form of deference indicating that the speaker was pleased to act in the manner that precipitated the "thank you" to which "prego" was the response.
I recall coming down to breakfast on the first morning of our honeymoon in Sorrento.
"Prego?", our waiter said.
"Too early to say" my wife replied.
Kicky I thought prego was an Italian meat sauce.
I use Prego like the commercial meaning- ' It's in there.'
This still makes me laugh, all these months later..