The Constitution guarantees in Article 4, para. 1 and 2 the freedom for every citizen to have (or to not have) a religious belief and the right to exert this accordingly. It also guarantees the undisturbed freedom for each citizen to practice his/her belief within his/her respective religious community.

Likewise, the Constitution's Art 3, para. 3http://www.gesetze-in-internet.de/gg/art_3.html guarantees equal treatment for all people. No one shall be discriminated because of his/her belief or religious views. This applies equally to atheists.

The principle of equal treatment between citizens regarding religion/belief is governed by the General Equal Treatment Act. More information can be found here.