There are several formats that will work on the web all with their own strengths and weaknesses.
1- If you want to use the video in a flash site you will have to convert teh video to FLV format. I believe that if you have the CS2 suite it has a program called Flash Video Converter (the name might be a bit different haven't used CS2 in a while). You can prety much convert any Quicktime file s from FCP.
2- If you are going to display your video in an HTML page you could instead use a QuickTime file. Compressor can make a web optimized Quicktime file for you.
I would suggest importing your ".mov" file into Flash then render as a flash file and upload the ".flv" file to your web page