Freemasons are prohibited from discussing religion or politics at there gatherings, it is not a religious organisation and has members from many faith groups, including Muslim and Roman Catholic but atheist are excluded from membership.
If it is a secular organisation but allows in members with a faith, why are atheists barred?
From the pages of the UGLE:
"Membership is open to men of any race or religion who can have a belief in a Supreme Being and who are of good repute."
From reading the pages I don't see what's different about Freemasonry than any other organisation that does charitable work (e.g. Round Table etc). In fact the Freemasons limit themselves by requiring members to believe in a "Supreme Being". I suppose that's their loss as people who have no faith but want to contribute to society through some sort of organisation will choose one other than the Freemasons.