Rachel, it's probable to do with the word here, it's a pleasure to have you here. For example Rita gave a perfect example, thanks for accepting my invitation, it's a pleasure to have you here, you are an important guest ( sort of thing ). I hope it helps.

Imagine you have invited someone to an event. They accept your invitation and, upon their arrival, you can say, "It's a pleasure to have you here" (= I'm glad that you are here).