How did the word 'Atheist' became a bad word?

Answer 1

Answer

The Roman's regarded anyone who did not worship the Roman gods to be atheists. They believed that atheists not only risked the wrath of the gods being brought down on all an sundry, but were probably traitors as well. When Christianity became the state religion of Rome, it suited the Church to continue to stigmatise anyone who refused to worship God - Atheism was simply not permitted.

Atheism is now acceptable, at least in the Western world, and the word 'Atheist' is no longer considered a derogatory term.

Addtion

Another reason is because established religions (majority ones) don't want people to give up their particular faith because that leads to a decline in donations/participation etc. It's the same reason almost every religion tells you that if you don't follow their particular faith you will burn in hell etc.

Answer

I'm limiting my answer only to the USA.

Atheist became a bad word when Sen. John McCarthy made this speech. "Today we are engaged in a final all-out battle between communistic atheism and Christianity." Feb 9, 1950

This is the speech that launched the terrifying McCarthyism (see link) attacks upon many US citizen.

Note that Sen. McCarthy did not say Communism against Democracy or USA against Russia but in effect [Communistic] Atheist against Christianity