The reason it seems Weeden and Yates know how to use Hopkins better than Hoyer is because they don't know the offense as well. When in doubt, throw to the best hands in the league.
I think he's just been in the system long enough not to do it. The system preaches ball control. Lobbing it up to Hopkins all day will result in turnovers eventually. Also, I think knowing the system better results in audibles that change into better (hopefully) plays. Not knowing the system results in "oh, I'll just throw it to Hop."