A while ago, Egypt's Islamic government discussed the presence of atheism. It was referred to as a plague which should be prevented from spreading. However, last time I checked, atheism was a viewpoint and not a lethal virus.
Atheism, agnosticism and/or secularism are undoubtedly regarded as a threat by many in Egypt. But why would the legislature employ countless efforts to wipe out those who made these seemingly harmless personal choices? Not only is there a great stigma attached to being an atheist but stating one's lack of religious beliefs can easily lead to legal sanctions on the grounds of apostasy.
Religion as Society's Number One Pillar
In Egypt, religion appears on one's ID. Refusing to state religion or choosing something other than the three monotheisms is out of the question. As you can see, it plays a primordial role: religion insures belonging to a community and provides an identity. It makes people feel like they're part of a large, stable organism – a solid building structure.
Furthermore, as a Muslim or a Christian, you live and prosper within your own religious community. You all follow the same traditions and cultural practices, share the same vision of life. You're handed out a script which indicates how you and your peers should act. It becomes a lofty nest, overflowing with a pleasant sense of security. Therefore, religion pretty much sets the social norms.
If all are subject to predefined rules, it's easy to understand one's life stance. It's almost effortless to relate to members of a certain community and by extension, to control them, as Islamism wishes to do.
Irreligion Screams Danger
Any non-conformist behavior raises skepticism and disapproval merely for being different. When one is accustomed to a certain philosophy of life, it's difficult to grasp why and how there are deviations from one's standard life rules.
A Muslim can guess how his fellow Muslims think and therefore remains within his security zone. However, while confronting an atheist he will be unable to predict his interlocutor's behavior, let alone relate to it. It will be a step out of the lofty nest. We tend to be threatened by the unknown and perhaps exaggerate the danger it represents.
In addition to being threatened by the unknown, being unable to understand the other, renders one powerless. It is considerably harder for Islamists to influence the non-religious crowd with ideologies which suit the predominantly Muslim population. That's why atheists are expected to conform or be sanctioned, perhaps even discarded by being thrown away in a cell.
Bonding Over the Enemy
I also want to add that as herd-animals, human beings long to be part of a group. An effective way to consolidate this group is to find a common enemy. Religious communities aren't exempted from such bonding methods.
Egyptian atheists, who are difficult to identify and to count since openly admitting one's lack of religious beliefs has adverse consequences, became victims in order to strengthen the Muslim society's sense of community. They also make good scapegoats: just blame global warming on the atheists, we want to be rid of them anyway.
I used a recent example of atheophobia, or fear of atheism I've encountered, but the same pattern of behavior can be seen in numerous situations anywhere in the world. Vilifying atheism is an easy way for the religious to avoid the work of listening and understanding.