It’s a misture between Windex and DrDommBot’s answer. In many cases, such as in Star Trek: Voyager, the flicker is mostly the remind the audience that the person is simply a hologram. There’s a decent number of examples of this, i’m sure, though only that one is coming to mind now.
On the other hand, though, the director can use it to change the feel of the technology. Star Wars was an excellent example. R2D2 is all sandy and rusted and plain old by then, his displays are not that great. In minority report, the holograms are flawless, to underline the ‘flawlessness’ of the whole society at that point. Another example I can think of is the hologram in ‘The Time Machine’ (horrible movie, btw). He’s very old, and the museum he ‘runs’ is falling apart and succumbing to the jungle. As such, he’s very jumpy, flickers a lot, and there are many places where he just doesn’t show, or only part of a display will show. Bad movie, but it did have some great points. :-p