I use a program called
FLVExtract which extracts the video and audio streams directly from the downloaded FLV file.
Hulu uses FLV as a container for h264 (video) with AAC (audio) in a FLV. (it might use other formats like mp3 for 360p video)
Then I use
YAMB with
MP4Box to repack it into a MP4 file.
No "conversion" necessary and it's a lot faster.