It depends on what I was hiring the person for. If I was an administrator for a religious charity organization, representing, say, the Catholic Church, then I may not want a vocal atheist to represent the church in that job.
However, in other types of jobs, I see no problem at all. As long as their beliefs don't interfere with their job, then I really don't care. Now, if I saw something terribly inappropriate on the internet about a potential applicant, then that would obviously effect my decision. For instance, lets say the atheist was being terribly disrespectful to those of belief. Then, yes, my opinion would be effected and so would be my willingness to hire.
And that would go for a religious person as well.
And for that matter, people can not hide behind their internet anonymity either. With that in mind, all should be mindful of their conduct not only in real time life, but in their internet activities as well.