He's 'having a rough time (of it)'. = He's 'going through a rough time'. [=he is having a difficult time; his life has been difficult recently]
The project still has a few 'rough edges'. [=the project still has a few things that need to be changed or finished]
Don't 'be so rough on them' [=don't punish or criticize them so harshly] for making a mistake.
(..) Yeah. I seen you around. You're Marty McFly's kid, aren't you? - Biff? - You're Marty Jr. Tough break, kid. Must be rough being named after a complete butthead. What's that mean? Hello. Hello. Anybody home? Think, McFly, think! Your old man? Mr. Loser? (..)1989 Back to the Future Part II