They were (and still are) a fraternal organization descended from the guilds of stonemasons who began to accept gentlemen into their ranks for their patronage, until they became purely "speculative," that is, consisting of non-workman. An anti-masonic pamphlet published in 1686 puts the early objections into focus:

"For this devillish sect are Meeters in secret which swere against all without their Following. They are the Anti-Christ which was to come leading them from Fear of God. For how should they meet in secret places and with secret Signs taking care that none observe them to do the Work of God; are not these the Ways of Evil-dom?" --Early Masonic Pamphlets, ed. D. Knoop, G.P. Jones and D. Hamer. Manchester: 1945, p. 34.

The Catholic Church was especially against secret societies. As Freemasonry expanded and developed a free-thinking philosophy based on religious tolerance and democracy, the Popes opposed it with increasing vehemence.

At the end of the 18th century, two authors John Robison and the Abbe Barruel, linked Freemasonry with the anti-clerical Illuminati and the French Revolution and Jacobism.

In the United States, despite the membership of such founding fathers as George Washington and Benjamin Franklin, there was resentment at the prestige of the masonic institutions and fear that their secrecy was hiding something. In 1826, the Morgan Affair set off a moral panic that nearly eradicated freemasonry in the US for a time. It led to the formation of the Anti-Masonic Party, which specifically opposed Andrew Jackson, a well-known and controversial mason. Ironically, their presidential candidate, William Wirt, was known to be a former freemason.

Not history, or a historian, but I invite you to talk to us over in /r/freemasonry. We're still around, and we don't bite :-).