"Are" always is a form of "be." Here's what you might be misunderstanding: every sentence in English needs a subject. We can't omit the subject like in the Romance languages: Há uma escola. Há duas escolas. Tem uma escola. Tem duas escolas. So sometimes "there" is just holding the place of the subject with a form of "be" serving as the verb. We use this structure when we want to say what exists or existed. There is one school. There are two schools. There was a school. There were two schools.

There are and there is, are the equivalent of tem or ha in Portuguese. There are horses. There is a house. In English there's a difference between plural and singular.