In 1738, the Roman Catholic Church issued an official document entitled In Eminenti Apostolatus that banned Catholics from becoming Freemasons, and the Catholic Church has been one of the leading critics of Freemasonry ever since. The 1983 document Quaesitum est is the Vatican's most recent document concerning Catholic membership in Freemasonry. In it, the Church has declared the following:
"The faithful who enroll in Masonic associations are in a state of grave sin and may not receive Holy Communion... the Church’s negative judgment in regard to Masonic association remains unchanged since their principles have always been considered irreconcilable with the doctrine of the Church and therefore membership in them remains forbidden."
All of the Papal Bulls (official Vatican documents which are directly from the Pope) regarding Catholics and Freemasonry are fairly ambiguous and somewhat unclear as to why the Church opposes Freemasonry. Many of these documents simply state that the Church's ban on Freemasonry is still active and that Freemasonry is a mortal sin in the eyes of the Church.
It seems that the Catholic Church's position on Freemasonry is unsubstantiated and that the Church is simply afraid of the power and prestige of such a large secret society. However, to find the reason why the Church bans Catholics from joining a Masonic Lodge one does not need to analyze official Church documents but, rather, look at how the Freemasons themselves describe their society. According to the Freemasons, "Freemasonry is not a religion, nor a substitute for religion. There is no separate 'Masonic deity', and there is no separate proper name for a deity in Freemasonry." One of the requirements for entrance into the Society of Freemasons is the belief in a Supreme being, and this in itself is very open-ended.
By observing this, one could conclude that the Freemasons are not only tolerant of all religions and beliefs but also believe that all religions are true. In many ways, Freemasonry inherently seeks to merge all religions into one. The Freemasons themselves will never declare that this is the goal of their society, but I believe that this is true of the Freemasons.
Of course, the Catholic Church will never accept any sort of compromise of Catholic doctrine. The Vatican will never agree to throwing away certain aspects of Catholic theology just so that Presbyterians and Catholics can be friends. The Catholic Church isn't simply afraid of a secret society. The Church just does not want its members to become soft - to become a cafeteria Catholic who picks and chooses which aspects of the faith he or she will believe and participate in and which aspects he or she will not.
You cannot say that you are a Catholic and choose to go to Mass only when you feel like it. And yet, you cannot say that you are a Catholic if you blindly follow the Vatican like a dog on a leash. The Pope isn't there to boss us around, and babies aren't there for us to kill just because we don't want them.

This was very interesting. I had no idea why the Church looked down upon Freemasonry, but now I have some idea. I agree with your reasoning. Allowing its members "to become cafeteria Catholics" wouldn't work. One cannot call themselves a vegetarian if they only avoid meat for five days of the week. People should choose to be Catholic, or any religion, because their beliefs match the beliefs of the religion, not because they like one aspect of it. It's kinda of a package deal.
-JenniferDylan
The "Quaesitum est" said that Freemasons can't receive Communion. How do they enforce that?
Denying an organization simply because its membership consists of believing in a supreme being of any religion doesn't seem out of the ordinary for the Church to do. The Church is very strict in its teachings and is sometimes, in my opinion, very narrow- minded in regards to other belief systems. Another reason why the Church would excommunicate free masons would be that their society is secret. We all fear what we don't truly understand, and therefore the Church would as well.