Is it permissible to work for an atheist who treats people well and allows time for prayer?

If your field of work is permissible, then it is allowed to work for a dissenting individual while fulfilling the duty of calling to Allah with wisdom and good counsel. Perhaps Allah will guide him through you, in accordance with the Prophet's (peace be upon him) saying to Ali: "By Allah, for Allah to guide a single man through you is better for you than red camels."