This because you have not stated the join condition between banners and website tables. For example
SELECT * FROM banners , website WHERE banners.websiteid=website.id
AND Bannersize = '$Bannersize' and website.Rating < 2 order by rand() limit 1";
If you don't indicate some sort of join condition between the two tables, you return a 'cartesian product'...all teh banners, all the websites