Though this is a minor point with regard to terminology, I'll begin by mentioning that if we're discussing Macbeth, it was actually during James I's reign that the play premiered. Therefore it was a Jacobean rather than an Elizabethan audience that first experienced it. But the answer to your question is that, in my view, there would have been a wide range of reactions among the theatergoers to the concepts of witches and witchcraft.
England and Europe as a whole were in a period of transition in the 1600s from the remnants of the old feudal order to a world in which the elements of our modern social order were coming together. The educational level of the urban population, especially, was rising. Huge advances in people's understanding of the universe had occurred with the work of Copernicus and others, and in England men like Francis Bacon were bringing what we call the "scientific method" into the public consciousness. I mention all this as an indication that a large number of people in Shakespeare's time would have known that a belief in the existence of witches is merely a superstition, and would therefore have seen the witches in Macbeth, and the supernatural elements of the play overall, as merely symbolic and not to be taken as literal or factual. That said, we know of course that a great many people still did believe literally in witches and demons. The Salem witchcraft trials occurred toward the end of the 1600s, albeit in America, where ironically religious fanaticism was perhaps more intense than in the mother country. But it was not until the early 1700s, a century after Macbeth, that the last executions of women alleged to be witches took place in Britain.
The witches in Macbeth are only one segment of the general presentation of magical and supernatural elements in Shakespeare's plays. George Orwell wrote, in his essay "Lear, Tolstoy, and the Fool," that although much speculation has been made in the critical literature about Shakespeare's religious beliefs, it would be difficult to prove on the basis of his plays that he had any. But whether he did or not, as with literature in general the central point is that religion, spiritual matters, witchcraft and the supernatural are all open to interpretation in the plays. And just as now, some people in Shakespeare's time would have taken the witches (and the ghost of Banquo, and so on) literally, and others would not have. The fact that there are multiple ways of looking at it is another sign of the greatness of Macbeth.