No they're not. 5D's airs at 6:00 on Wednesdays on TV Tokyo. Also on TV Tokyo, Gintama is on Thursdays at 6:00 and Bleach is on Tuesdays at 6:00, and ratings-wise, they both consistently blow 5D's out of the water, sometimes even doubling what 5D's does. There's the odd week where 5D's does well, but overall, its ratings are subpar no matter how you slice it. There are weeks where it's the lowest-rated anime airing on TV that's not a rerun or on at a time like 2:00 am. Hell, there's the rare week where it gets beaten by a GX rerun.
But of course, I agree that since it's a toyetic series, and TV Tokyo probably gets some kind of cut of the card sales, that ratings aren't the only deciding factor. If they were the only factor, the show would be gone by now. But TV Tokyo is a television network and they certainly care about the ratings somewhat, so I don't know if they'll put up with the lousy nurabers forever.
The most likely thing to happen though is that the next Yu-Gi-Oh! series will get a lesser timeslot. Like how Bleach was moved out of its prime slot a year or two back (I think, I may be wrong here).