66 doesn't equate with 666. But the number 6 was regarded by the Jews (and later the Christians) as a number representing imperfection. Why? Because 6 is one short of 7, the number representing perfection (deriving from the days of creation in Genesis).
Hence, the number 666 is regarded as representing evil since it's a triple imperfection.
Christians also regard the number 3 as symbolizing good because it represents the Trinity. Therefore, it's more than interesting that Luther's canon is comprised of 66 books (doubly imperfect) while the Catholic canon is comprised of 73 books (two numbers representing perfection).
An interesting aside. I once worked for a company called the "37 Design Group." I asked the owner, who wasn't particularly religious, why he chose the numbers. He said, "because they're everybody's favorite numbers."