those lines are because the footage is interlaced. normally, like when you play it back on a tv at full quality, you wont notice it at all, but since its compressed you can really see it pretty bad. so just de-interlace your footage in post. though sometimes even when i do deinterlace in post, and i put the footage on some website, it goes back to interlaced footage for some reason.
you can easily deinterlace in fcp.
i use this alot though http://www.xs4all.nl/~jeschot/home.html#DEI
it makes your footage alot smoother and when slowing footage down its alot smoother too. better than normal deinterlacing for sure.