Do you think Sam's dad knew about her + his boss?

This bugs me too.

I really want to know what had happened to Sam. Dis the boss abuse her?

That film is titled The Perks of being father to a daughter molested by your boss.

my vote history:
http://www.imdb.com/user/ur13767631/ratings

I do not think he did. The movie takes place in 1991-1992 which means her father's boss kissed her (and maybe did more) in 1984 or 1985, since she said she was 11. In the 80s and 90s when someone was accused of molesting children, people usually reacted saying "no way," or "impossible." People literally had to be caught in the act for people to believe the did such horrible things. I doubt she mentioned it to her father and would be surprised if he ever suspected.

I’m actually willing to bet he did know—that Sam went to him about it and he didn’t believe her—and that that’s largely why the two aren’t close. Early in the film she even describes him as “worthless.”