It implies that things are not always what they first appear to be. You could just about apply this line to any murder mystery that you have ever seen. The murderer is always the person that you least suspect. Good is bad, and bad is good.
Macbeth first appears to be good. He's honored by King Duncan for his prowess in battle and major contribution to the overall victory. But as the play continues, it is clear that Macbeth is indeed not nearly as fair as he first appeared. Conversely, Lady Macbeth is evil at the start of the play. Some readers even think that she deserves more blame than Macbeth himself. But I do want to give her some credit. Her guilt absolutely consumes her. She doesn't turn from foul to fair and pure as the driven snow, but at least she expresses a hefty amount of remorse.
The line also implies to the audience that they just shouldn't trust what the witches say word for word. Macbeth learns that one the hard way when Birnam wood comes marching to his doorstep and Macduff is able to kill Macbeth because Macduff wasn't "born" in the traditional manner.