Martin Luther, of course, got a lot of credit for The Reformation, but I think it's no accident that The Enlightenment seems to include The Reformation as a huge feature. Of course, another huge feature was the scientific method, and another huge feature was classical liberal government (there were others, such as movable type, which Luther famously exploited in producing the Gutenberg Bible.)
If you think about it, they're all intertwined. Luther did not mean to be excommunicated and start "protestant" christianity, but rather to reform the church. Classical liberal government is of course a reformation of a sort too, and certainly the scientific method is a continual reformation of observation and the ideal response to it.
I think that's a major way liberty, science and (oddly enough) religion can be related. The skeptical approach that says "give me a reason to believe as you, but don't force your way on me," (this is not to contradict the business about the Holy Spirit, which is beyond the scope of this) and it seems to merge that whole enlightenment discussion and (at least, classical liberal) thoughts on liberty.
Back to Luther, though, you can't get a lot more individualist and civilly disobedient than to stand at the
Diet of Worms, threatened with perhaps torture or the death penalty (and probably would have been if not "kidnapped" by Prince Philip and protected for his remaining life), refusing to recant your personal beliefs, which you believe you've backed by the Bible (think: Constitution; think: Natural Rights; think: that which cannot be justly or wisely contradicted):
"Here I stand; I can do no other. God help me. Amen." This is individual rights stuff; the right to believe and teach as you conscientiously determine is "The Truth..." and if it's not the truth, it's still your right to believe and teach it, and it's someone else's right to contradict you and provide his own evidence.
WRT Judaism, I've heard similar things said of it to that of Lutheran education, and I've seen enough of it to recognize that there may be truth to that.
That's either brilliant, or I've had too much medicine to type shit like this, or somewhere in between. It's not original--it's basically what I learned in one of my civics classes when we studied The Enlightenment, enhanced by my earlier religious education. I guess I was lucky I didn't get the typical left-wing spiel from college.