I don’t think they are a legitimate religion.
You are right that Freemasonry isn’t a religion, but I don’t think that that invalidates my point. The Freemasons themselves would say that their way of life can encompass all religions, including Catholicism (I asked them about this, and they said that while Catholics tend not to join because of Church teaching, the Freemasons themselves are perfectly happy to allow Catholics to join). The only requirement that they have is that people wanting to become Freemasons have to profess belief in a supreme being. They will never ask in exactly what supreme being people believe, and they do not discuss religion during lodge meetings.
From what I have found out about Freemasonry by visiting the United Grand Lodge of England and talking to people who are Freemasons, it could be characterised as a system of beliefs and practices based on belief in a supreme being and the use of myths, symbols, and rituals to express their guiding principles.
I don’t think that a set of beliefs, a way of life, or a community of people necessarily has to be what you call ‘a legitimate religion’ for it to enjoy the right to be treated with tolerance and respect. The Scouts are not a religion, but they share a number of characteristics with Freemasons. The Scouts, for example, make it a requirement that members should profess belief in God or something similar to belief in God, e.g. Buddhism. However, the precise nature of this belief is not prescribed, and people practising a wide variety of religions are able to become Scouts. The Scouts also use symbols and rituals, such as the Scout sign, the Scout salute, saluting and honouring the flag, and using phrases such ‘Be prepared’ and ‘Do your best’. Scouts have an initiation ritual involving the making of a promise and being invested with insignia appropriate to membership and rank. Cubs use a mythology based on Kipling’s
The Jungle Book, in which every Cub is identified with Mowgli and the adult leaders are identified with the animals who in the original story help to guide Mowgli towards manhood.
I would only be inclined to be concerned about Freemasonry if I thought that they were involved in conspiracy to commit misconduct in public office, perverting the course of justice, etc.