1. The availability of the flash runtime, so you can do other
things besides only display the video (including customized display
of cue points, overlays, etc). You are often able to make smaller
files with the FLV encode than with the MOV encode.
2. Yes. Many 3rd party encoders give you more functionality
than the default Flash encoder, including embedding cue points.
Also, it is debated that you can get a smaller file at a better
quality with some third party encoders vs the default Flash
3. No. There are things that you can do to make it more
difficult, but, as with anything posted online, there is no
sure-fire way to keep people from getting it.