"It's nice to be back" is a set expression that people use when they return to somewhere.
In the sentence above, the speaker stresses the word "be". That's because "It's nice to have you back" is almost the same sentence. The only word that's different in the response is "be". In English, when you repeat a phrase or sentence, you usually stress the words that are different. Another example:
A: "Hi, it's nice to meet you."
B: "It's nice to meet you, too."
In this example, you emphasize "you" in the second sentence. Even though the word is the same in both sentences, they're referring to different people. When Person A say "you", he means Person B. When Person B says "you", he means Person A. So "you" is stressed in the second sentence.