Do you enjoy your work?表示你对工作的整体感受是不是enjoyable.
Are you enjoying your work?表示你此时对工作的感受是不是enjoyable.如果你此时工作不顺利,遇到些麻烦事,可是总的来说你还是觉得工作是不错的,可以说：
Although I am not enjoying my work this couple of days,I still enjoy it in general.Difficulties are temporary.