What could be simpler.
Open TubeTV, which is a web browser with the same guts as Safari.
Paste in the URL of a page containing a flash movie.
Click the flash movie to start playing it.
Now the download button becomes active; click it.
TubeTV downloads the flash video.
TubeTV converts that to a movie file suitable for for iPhone.
TubeTV opens the movie in iTunes.
Now I check the box in iTunes that says I want it on my iPhone for bedtime watching and sync.

Of course, you can choose a different conversion format and set other options.