Flash vs Compressor

Hello to all...
I am looking for advise on making the right choice here. I know this is the flash part of cow but I am hoping that someone has had some experience in dealing with both Compressor and Flash. What I am about ready to do is start a website site that will mainly be video heavy. We are going out in our area to promote businesses and get deals for people in our area. The response to the idea is huge and people love it. What I would like to know is will flash be better than compressor in the long run? I don't own flash but I do own compressor but I have been trying to export files from compressor and the footage after a 2.5 render comes out very interlaced you can see the lines and so fourth. Yes I did have de-interlace on. I am NTSC using a Canon xl 2 and a Sony fx 1. Can anyone help point me in the right direction.

Thanks
Chuck