You don't. You convert your mov file to a mp4 h264 encoded file, and import that into Flash. Then export to swf (in a folder), and you use that swf in your page (do not forget to upload all the other assets as well).
Alternatively, convert to html 5 video files which are also supported by mobile devices.
Learn more here: http://diveintohtml5.info/video.html
ps you can use the Adobe Media Encoder to convert your mov files to h264. Or to html5 video: