Why are atheists looked down upon or considered bad people?

For some people morality is so tied up, conceptually, with organised religion that they don't see the former without some indication of the latter. Religiosity, for them, has become a test for morality. Another side of the issue is that when there is this hostility towards atheism, it creates a reaction among people who are atheists, and some of them will become obnoxious in their turn. There are these vocal atheists around who think spirituality should be abolished altogether, and instead of promoting that end it just creates a self-fulfilling loop of animosity between atheists and theists.