As mentioned above, the audiences of Shakespeare's time would have taken the threat of witches very seriously. The period between the 1400 - 1700 AD in Europe is known as the classical period for witch hunts and witchcraft trials; marked specifically by the trial of Joan of Arc by the English at the beginning of the period, and the hysteria and trials of the Salem witches in 1692 in New England at the end of the period. Specific laws against witchcraft were passed in England in 1563 during the reign of Elizabeth. Many people of the time had an almost hysterical fear of witches and would have found the witches in Macbeth quite scary rather than somewhat humerous as they are often considered today.
Since we'll never know for certain how the audiences would have acted seeing the play we have to examine the history and cultural norms surrounding the Elizabethan time period.
Most people during this time period did in fact believe in witches so the audience's reaction to the opening scene and subsequent scenes with the witches were, most likely, taken very seriously. The audience would have reacted more emotionally than audiences do today to the witches on stage. They also would have contemplated what was being said by the witches much more closely. The concept of Evil was a very intellectual topic during this time period. The audience would be frightened and intrigued to see Evil manifested physically on stage by the witches.