re: Why does the word "profit" have a negative connotation?

Short answer:

Profit-motive is just that: motive. It's the motive that has built and sustained any vibrant economy. Humans wants to improve their condition and want to have more. For the most part, it's a selfish ambition, but it's side-effects naturally improve the condition of others.

However, the phrase "money is the root of all evil" didn't just pop up out of nowhere for no reason. People will do F'd up things to make a buck. Not saying that is the case with many for-profit organizations, but that's why you see the movie plots centering around it.