I think it looks trashy, I spend all that time to make my tank look nice, don't want to see a stupid magnet hanging off it. Little things like that help the tank as a whole look better.
I also don't want crap growing on it... If you leave it in there, tubeworms etc will grow on the underside and I'm afraid they may scratch the glass. And lastly, there are numerous stories of them being less than watertight...
Oh, and for some reason, if you leave it in the tank, it's the only thing people notice when you show them the aquarium. Ignore the beautiful fish and corals, that magnet is AMAZING lol.